I have a wacky idea that may work for you. Basically you need a midi out that would show up before the soft synths. So why don't you download and install LoopBe1. It's free. SONAR would see it as hardware so it should be first on the list. And it is pretty darn useful.
Worth a try.

I dont see the problem. I have MANY keyboards all working as controllers. All have their names on the list. Nothing gets massed up. I have them on some time, another time, I do not. Sonar asks me, "Yamaha Motif was removed, do you want to reassign MIDI Inputs?" I say NO and everything stays in place. 

vlad, my bad, I was trying to make the scenario as simple as possible for the purpose of creating this thread.  The reality is I'm not removing a card from an existing system, rather I built another system which doesn't have an SBLive card any longer.  So, true, what you are saying might work for a situation where you already have a machine configured that matches existing projects.  But in my case I have a new machine that is now missing the first MIDI device so everything in the track output selections is shifted incorrectly when I open the projects.
 
Base57, that suggestion makes sense. Come to think of it, I might be able to use one of the already existing MidiYoke outputs (which seems the same concept as LoopBe1). That might however put things at risk for a nasty feedback loop were I to accidentally select the wrong IN/OUT combination on a track.  I wonder if that's a potential system damage concern or not?
 
BTW, is there a way to rename I/O devices in S5 PE?  I'm not seeing anything obvious, unless it can be done via an INI file...

I switched to new computer this year as well. Every time I open old project that had something I dont currently use, it asks me, "MOTU MIDI Output and Input are missing, would you like to Reassign?" I say no and it just silencing the missing tracks. Also there is a setting for Friendly Names, I dont know if it applies to MIDI or only Audio, but all my inputs are marked. I have at least 10 controllers, and i will assure you that I dont use them all at the same time, but they show up in the options if the driver is installed. If the driver is not installed but the project had that assignment, it simply asks me if I want to reassign. I dont like to let it reassign, so I say NO and reassign myself. How hard can it be to reassign Inputs when you need them? Most likely you only will need to reassign few inputs per project. Also I commit my tracks to Audio, I almost never keep anything in MIDI. Yes, I may want to change it later but I make my decision when I work on that part. So I have 80% audio. The only time I have real issue with not knowing what is what is when i set my Metronome to MIDI on certain MNIDI out, let's say Out 6, and I have to remember that it is 6th module in my hardware synths rack, and it gets massed up and some time it is 4, some time it is 5. So I started using Audio click. 

vlad, keep in mind I'm using S5 PE, it may not have that behavior/functionality you mention.  And in my case, between the drum synths and keyboard tracks I have 15-20 MIDI tracks per project I'd have to mess with.

As I said, I don't think any of us understand what your problem is. We totally get that you have changed your system and we all totally get that this will result in what you are describing but we don't get what your "problem" is with that. 
 
question- are you using VST soft synths at all? or are you trying to use MS wavetable or external hardware?? I have a feeling your troubled because you were using the sound fonts on the Sound Blaster and now they are gone//right? 
 
As I said, Sonar will open old projects on a new system no problem other than the plug ins may no longer be available so it warns us as it loads and then they show but are greyed out. You either find the old plug ins and install them or you replace them with something more up to date. 
 
Inputs as I said, so what if they show in a different order.. why does that matter, I can't think when this would cause a problem. 
You just choose the controller your going to use to record with. 

Cactus Music
As I said, I don't think any of us understand what your problem is. We totally get that you have changed your system and we all totally get that this will result in what you are describing but we don't get what your "problem" is with that.

Well, some people understand what the problem is...
There is a BUG in Sonar. I am not sure when exactly it was introduced, probably in the version when they have made MIDI ports "more persistent".
 
Sonar identify existing MIDI ports by names. That is a questionable decision by itself (f.e. the reason why more then one instance of some USB-MIDI devices is impossible to use), but it has one logical advantage: if you let say have "MY_MIDI_DEVICE" and use it as MIDI input on some track (for using more then one controller in parallel, fighting with "MIDI Leaks" Sonar bug, etc) or as a Control Surface, you can expect "MY_MIDI_DEVICE" will be set as the input even when MIDI configuration is changed, as long as "MY_MIDI_DEVICE" exists (or re-appear) in the system. Unfortunately, that is not the case. That is clearly a bug. And that is a problem for OP.
 
I (and many other) observe this bug (with hi probability the same, but I am not 100% sure) in a more weird way. If "MY_MIDI_DEVICE" is assigned as an input for some Control Surface plug-in, after MIDI configurations is changed, it is still shown as the input for this plug-in. So everything looks good. But it only looks good, in reality the input is shifted to some other device... Temporarily re-assigning the input to another port, apply, assign to correct one most of the time fix the problem. In worse case, INI files wiping is required.
 
For someone the workaround with "fixing" assignments is not a big deal. In other that is rather annoying. I think it is incorrect to claim that no one see that as a real problem.

azslow3

Cactus Music
As I said, I don't think any of us understand what your problem is. We totally get that you have changed your system and we all totally get that this will result in what you are describing but we don't get what your "problem" is with that.

Well, some people understand what the problem is...

Im with Johnny, I have no idea what the problem is.
 
The problem he is trying to solve here is with Sonar 5 in Windows XP.(perfect example why we need a sonar legacy forum)
 

azslowThere is a BUG in Sonar. I am not sure when exactly it was introduced, probably in the version when they have made MIDI ports "more persistent".

 
If there was a midi bug introduced here, we are talking about a 10 year old midi bug. 
Im not even sure there were .ini files in Sonar 5. that's why I dropped out of this thread.
However it may seem what Johnny is saying is of no use.. it might actually help.
Because the issue can be described in better detail. Thus more of us may understand a little better.
 
Though I believe if anyone can help Sonic solve this issue it would probably be you because of your knowledge of midi.
 
 
 

Thanks Chuck for backing me up as I think both of us would truly like to help the OP but so far I just don't see why ins and outs changing is a problem. I'll admit I not using a lot of in's and out's and maybe it is an issue for someone with a very complicated set up but for me it only takes a minute to fix this. To expect the Software to figure it out seems like asking a lot.  And to complain about OLD versions will fall on deaf ears anyhow.  
 
I have 3 midi input devices and these have all changed over time as I upgrade. 
If I open an old project, and some of these were made in Guitar Studio which I think is same era as S5 and S6 they might go looking for my Sound blaster card and things are not going to work right away until I do a little bit of work. As I said,,, I would expect this when you try and open any old projects. 
If you don't like this then I guess you just never upgrade your system. 
I really wonder if the input and output assignments would behave the way your asking in any DAW? 
 

Everybody relax. lol  I really appreciate the help, truly. If there isn't a solution, then there isn't a solution.  I'm just trying to understand what the options are.  I can't see how anyone can say they don't see the problem though.  To say it's not a problem in their opinion is fine, but to say they can't see the problem I'm referring to is very perplexing.  I spelled it out about as clearly as can be (in particular see post #7).  Sonar seems to track the ordinal/position of the MIDI output selection in the track output listing instead of the actual proper output selection when it comes to the configuration changing.  Sonar really should be tracking by name or some other internal ID, anything that allows it to retain the proper mapping.  I don't care how old the software is, it should have the basic intelligence to at least be able to maintain the previously selected output (provided it still exists) on a new system or configuration.  
 
It sounds like Sonar is hopeless in this sense and the only way to potentially resolve this is to make sure some kind of placeholder remains in the initial location where the SBLive used to be.  Whether it be putting the SBLive back in the machine or use a virtual software stub (MIDIYoke, etc).  

If anybody has any other ideas please share....
 
Sonic