Well it has MIDI output like my GR 50. I'm not sure this has all been mentioned but all you need to do is is run the MIDI output to your interfaces MIDI input. I don't see an interface in your spec list so not sure if you have that option. If not then you will need a audio interface with midi ports. 
Then all you do is insert any Synth and play it. There will be the same latency as your getting from the MG set up however. But if it records all the notes and strings this would prove that your GK PU and cable are working and only your GR20 is hopped. 

MGMitchell
So is there a way to use my GK3 pickup (that I already have for the GR20) to input directly to midi VST instruments and bypass the "Midiguitar" FX? I assume that would help with latency.

No. The GK3 has a separate humbucking PU for each string. The output is analog, just like a regular humbucker. A vst instrument needs midi input. Johnny V makes a good suggestion, although if there is a problem with GR20 it wouldn't surprise me if it's at the input stage. Still it's worth a try.

If you're interested in GTR-To-MIDI the Boss GP10 is worth looking at. It doesn't have have built in PCM sounds, but it does quit a bit and people seem to like it. Without a PU street price should be $350-$400.
 
http://www.bossus.com/products/gp-10/
 

 
The GK 3 is the newer version of my GK 2. It is not a humbucker and it does not transmit analog per say, it wires directly to the GR 20 with a multi pin cable. If the PU or the cable are faulty the GR 20 will not play properly. This is what my issue was. The GK 2 was not working any more and I lost a few strings. I thought it was the cable but the cable is working fine with the Godin. 
The only way to really test things is to swap out parts. I really think it's the PU or the cable even though you had it tested. The only way to test it is to use another midi guitar controller that has the multi pin connection. DO you have a music store nearby? 
 
The first thing I would try is to reset the GR 20 to factory. This will eliminate the possibility that you have change a setting. With mine it is not hard to be in the wrong mode and shut the sesitivity off. I have some old patches that I shut strings off on so it would only play the top 4 strings as example. 

I love that the TriplePlay is wireless for MIDI

Cactus Music
The GK 3 is the newer version of my GK 2. It is not a humbucker and it does not transmit analog per say

Yes, it does.  The GK-3 uses 12 of its 13 pins:
 
6 pins for the 6 analogue divided pickup signals
1 pin for the original guitar analogue signal
2 pins for the buttons
1 pin for the volume control
2 pins for +/- supply voltages
 
The 13 pin plug design is pretty poor and is susceptible to strain; if you've been using it for some time without providing any strain relief at the guitar end, it's possible that some damage has occurred on some of the divided pickup signal pins (in the pickup's connector, not the cable).  It'd be easy enough to test each of the divided pickup's signals on the pickup's socket.
 
This is the only wiring diagram I've found thus far:
 
http://i412.photobucket.c...-55/GK_VOLSET_PLUG.png

In terms of the technology of the Roland hexaphonic pickup. From the Roland GR-300 -
"One Roland guitar synthesizer technology innovation is the world’s smallest humbucking pickup.

Each element in the Roland guitar synth pickup is actually a tiny humbucking pickup. As you can see, the patent illustration (on the left) depicts a classic humbucking pickup, with dual coils wrapped around opposite magnetic poles. This configuration cancels out noise while amplifying the essential guitar signal. By using tiny humbuckers, Roland was able to apply the incredible amounts of gain needed to take the tiny microvolt output from the pickups to a 25 volt, peak-to-peak signal used to directly drive the Voltage-Controlled Oscillators in the GR-300.

Interestingly enough, the earlier GS-500 used what appears to be a collection of six tape machine pickup heads to make the divided pickup. With the G-303/808 Roland introduced the divided hex pickup design still in use today, with minor modications."
 
That is from Joness' web site that has a lot of information on early Roland synthesizers. That technology went into the GK 1 divided PU and then GK-2, GK-2A, and GK-3.
 
http://www.joness.com/gr300/GR-300.htm
 
Scroll down to the bottom of the page for the information on how the GR-300, including PUs, works.
 
"The GK-2 pick-up is the same pickup as the Roland GK-1 pickup, offered as part of the Roland GK-1 kit which included the GK-1 pickup, GK Driver and special 24-pin cable. The GK-1 was the last of the original Roland 24-pin hardware. Unlike previous Roland guitar synthesizer pickups, the GK-1 was designed to be easily added to the top of any guitar, without requiring any special routing. The GK-2 was released in 1989 with the Roland GR-50. Shortly after the original GK-2 shipped, Roland released the more familiar GK-2A pickup. The GK-2A pickup was more versatile than the GK-1 (or GK-2) pickup, and could be installed either on top of the guitar, or internally installed. The GK-1 (or GK-2) did not lend itself to internal installation. The GK-2A was used as the factory hardware on the Roland-Ready Stratocaster. The GK-2A was replaced by the GK-3 in 2005. The GK-3 pickup is the factory installation kit for the Roland GC-1, GK-Ready Stratocaster. All Roland pickups are actually made up of six, small, individual humbucking pickups to allow the output of each string to be processed separately."
 
http://wiki.csisdmz.ul.ie/wiki/Guitar_Synths_%26_the_GK-2_pick-up
 
 

Yes  It's been a long time since I gave it much thought as I have had my GR-50 since 1989. I stand corrected about the term "humbucker" but it is certainly not the same thing as found on a regular guitar and no "sound" is heard from them. 
 
The Hex PU  signal is not used to reproduce the actual guitar sound on the GK2 system. I cannot speak of the GK3 but I assume it works the same way.
 That's why I said " no analog sound per say" because there is no "guitar" sound sent from the Hexiphonic Pick ups, The actual guitar signal is from the regular Pups which are patched in with a short cable. The Hex PU is used for the synth only.
But:  
There are systems like the Godin that use the same pick up for a accoustic type sound and the multi controller send for the Roland GR systems. I new a Luthier who custom installed these ( Graph tech??) saddles. They would then hobble the guts from a Roland GK into the wiring. 
So with my old GK 2 If I used the short patch cable my guitar sound was send to the back panel jacks. There is the mixed signal in stereo or the individual guitar output that you send to your amp.  
It was not a great way to go as the multi pin cable is crap and tends to crackle. I always used a regular connection direct to my amp. There is a noticable loss of gain and tone if you use the multi pin. 
The Godin has 3 outputs and is very versatile yet complicated. . 
 
From Godins web site: 
So we began experimenting with the idea of a guitar built from the ground up with synth tracking in mind. Our old friend Richard McLish of the RMC pickup company already had developed a hexaphonic pickup and preamp system called the RMC Polydrive and we asked him to work on a version of his system customized for our new guitar, which we called the Multiac.
 
My sons Godin  =   http://www.godinguitars.com/godinxtsap.htm
The xtSA delivers big time electric sounds via the Godin humbucker-single-humbucker pickup configuration and thanks to a special 5-way switch setup extra meaty humbucker tones co-exist with glassy split-coil sounds in the second and forth position. Turn down the electric output and raise the volume on the RMC transducer saddles and the xtSA becomes an incredibly authentic-sounding ‘acoustic’ guitar. The acoustic voice of the xtSA is enhanced by an onboard preamp with a three-way graphic EQ. The two outputs are set up so that the electric and acoustic voices can be blended in the guitar using a single patch cord or at the amp/mixer using both outputs. The icing on the xtSA cake comes in the form of its synth tracking, which simply put, is the best in the business. As with all of Godin synth-ready instruments, a built-in 13-pin connector provides direct access to all Roland GR-Series synths as well as most other 13-pin devices.
 

Cactus Music
Yes  It's been a long time since I gave it much thought as I have had my GR-50 since 1989. I stand corrected about the term "humbucker" but it is certainly not the same thing as found on a regular guitar and no "sound" is heard from them. 
 
The Hex PU  signal is not used to reproduce the actual guitar sound on the GK2 system. I cannot speak of the GK3 but I assume it works the same way.
 That's why I said " no analog sound per say" because there is no "guitar" sound sent from the Hexiphonic Pick ups, The actual guitar signal is from the regular Pups which are patched in with a short cable. The Hex PU is used for the synth only.

You don't get the analog sound of the separate strings from your GR-50 or some other units, but if you use a break out box you can access the signal from each string.
 
http://www.separate-strings.co.uk/activebreakoutbox.html
 
Going back to the GM-70 and forward thru some of the GR's like GR50, GR33, and GR20, Roland did GTR-To-MIDI conversion, but in the VG series they were applying some form of wave-shaping to the signal. It's like the GR-300, but in the digital realm. That approach is more like an analog synth. The VG series, GR-55, and GP-10 do guitar modelling, altered tunings, 12 string simulation, and analog synths based on the analog signal from the separate strings.
 

Cactus Music
There are systems like the Godin that use the same pick up for a accoustic type sound and the multi controller send for the Roland GR systems. I new a Luthier who custom installed these ( Graph tech??) saddles. They would then hobble the guts from a Roland GK into the wiring. 
So with my old GK 2 If I used the short patch cable my guitar sound was send to the back panel jacks. There is the mixed signal in stereo or the individual guitar output that you send to your amp.  
It was not a great way to go as the multi pin cable is crap and tends to crackle. I always used a regular connection direct to my amp. There is a noticable loss of gain and tone if you use the multi pin. 
The Godin has 3 outputs and is very versatile yet complicated. . 
 
From Godins web site: 
So we began experimenting with the idea of a guitar built from the ground up with synth tracking in mind. Our old friend Richard McLish of the RMC pickup company already had developed a hexaphonic pickup and preamp system called the RMC Polydrive and we asked him to work on a version of his system customized for our new guitar, which we called the Multiac.
 
My sons Godin  =   http://www.godinguitars.com/godinxtsap.htm
The xtSA delivers big time electric sounds via the Godin humbucker-single-humbucker pickup configuration and thanks to a special 5-way switch setup extra meaty humbucker tones co-exist with glassy split-coil sounds in the second and forth position. Turn down the electric output and raise the volume on the RMC transducer saddles and the xtSA becomes an incredibly authentic-sounding ‘acoustic’ guitar. The acoustic voice of the xtSA is enhanced by an onboard preamp with a three-way graphic EQ. The two outputs are set up so that the electric and acoustic voices can be blended in the guitar using a single patch cord or at the amp/mixer using both outputs. The icing on the xtSA cake comes in the form of its synth tracking, which simply put, is the best in the business. As with all of Godin synth-ready instruments, a built-in 13-pin connector provides direct access to all Roland GR-Series synths as well as most other 13-pin devices.
 

 
The Godin's (I have an LGXT and ACS-SA) are a little different, they use piezo pickups, not humbuckers.