Okay, I admit, that's news to me that plugins aren't instruments. I just don't see how all this addresses my problem. I'll try to be more clear...
 
I have created "Instrument Tracks" by right-clicking in the Track View and choosing "Insert Instrument". When the "Add Track" box appears, I use the "Instrument" pull-down menu and choose an instrument, in this case "Cello" (whether it's a plugin or not, though they were all called VST Plugins when I got them). I don't mess with the Input or Output at all... then I select "Create" and the track appears. I play the part on Akai controller, all is right with the world.
 
Down the road, I add another instrument track (a Rapture synth), and I make a reference mix. I decide I don't like the mix and go back in to remix it, but I notice I'm not hearing the Cello, and the Synth sounds different. So I "solo" the "Cello" track, and even though I still can 'see' the Cello part's midi information, I don't hear the Cello, I hear the Rapture synth part, even though the synth track is not in solo. When I solo the Synth track I hear nothing. I open the "Plugin" window for the Cello track and see that it is not even using the instrument I chose, it is using the TTS-1 default. I reassign the track back to the original instrument I chose, but I still don't hear the Cello part, I still hear the Synth. I see that the Synth has also defaulted from the Rapture to the TTS-1, I reassign the track to the Rapture settings I used. Now I hear the correct "Synth" part, but only when the "Cello" track is in solo. I finally found my Cello part, but it is being played by a Strings track. I had two String tracks, but since the Cello is playing on one of the String tracks I have lost that second String part altogether. I'm trying to save this mix and don't know how to make the tracks I have already created play the correct parts. If your information does give me what I need to fix this and I just don't see it, then perhaps I should just go buy an old Porta-studio.

Cactus Music
...Soft Synth = VST instrument. They are not plug ins, Plug ins are effects...

 
Sorry, but you're wrong about that. Both softsynths and fx are plug-ins. The term doesn't just apply in the DAW world, but to software generally and usually means a software add-on.

I'm also having the same midi problems. never had in the past but somewhere - possibly around this last windows update in the fall - midi tracks would behave exactly as you described.  Honestly at the time I was more concerned with Sonar being dropped by Gibson and moving/starting new projects to S1 or Ableton where midi and softsynths work fine. But I have been going back to some old Sonar projects now and it's driving me nuts. I'll have to reassign synths/addictive drums to midi tracks to get them to play...and than if I go to another midi track I'll either hear the wrong instrument or it won't play at all. I've been having to get a midi track to play properly and than bounce it down to audio and erase just so I can work on another midi track.  Something is definitely wrong

If you delete a synth that is currently assigned to a track  or tracks  - that assignment will get re-assigned to another synth. It does not default to  (  none  ) or your default assigned midi port or sit unassigned.  It goes to the next synth on a stack list of sorts. When you want to re-assign a midi track to an instrument you definitely need to understand how to assign them - it's actually quite easy -. In the track view - or the track inspector -look for the box  with an outlined -   O  - , which stands for output. Open the drop down list and choose the available midi port or available instrument. Then double check the midi channel it's outputting on. Then worry about the particular patch.

If anyone else is interested enough, Cactus Music posted a great link here to a conversation with some good info, and I'll definitely be referring to it moving forward, but I can't glean from it anything that helps me fix my current issue... if any of you want to look at it and let me know if I missed something, that would be great.
http://forum.cakewalk.com/Issues-with-Sonar-Home-Studio-m3721656.aspx
 

I think Rbh has nailed the wrong synth issue.
 
If you delete a VST the midi track that was assigned that instrument will automatically be re routed to another available synth. 
It is no big deal to re assign synths. 
Here is the list of in/outs on a midi track PAY ATTENTION to these
 
I= Input,  This is need to record a new track, choose your midi controller and use OMNI. Make sure INPUT ECHO is highlighted. 
O= Output  direct this to the VST instrument
C= Midi Channel-  Most can be left at ch 1 but I personally use a different channel for each instrument.   
B= Bank most I set to NONE, depends.
P= Patch set the patch here or leave it at NONE and use the VST's GUI menu. 
 
If your hearing the wrong instrument when you play from your controller you need to see what tracks have input echo on. 

Sorry, maybe I'm just dull, I don't see how that addresses hearing the midi performance that's recorded on Track 13 when I have Track 11 in solo, and hearing the midi performance that's recorded on Track 11 when I have Track 10 in solo, or how to correct it... These tracks were created by the "Insert Instrument" option, when I look at the midi Input and Output, they are invariably "Omni", "Midi Omni", VrtlCntrl0" for input, and "Master" for output. Reassigning the Input midi channel up and down the options doesn't bring the correct performance to the track. I'd post a video if I could.

Could there be synth plug-in(s) with "Enable MIDI Output" enabled? If so, having MIDI tracks input set to All Inputs > MIDI Omni will pick up the MIDI data from the plug-in(s). The plug-in MIDI I/O options are visible in the VST2/3 drop down in the standard plug-in header and in the synth settings menu in the synth rack. "Enable MIDI Output" may set/unset by using the Insert Soft Synth Options dialog when adding synths to  a project.

I do find the Enable MIDI Output, in no instance I do find it "checked" or "selected", but the option is greyed out anyway. Enable MIDI Input is checked.

OK I look at your screen shot and I see things that don't seem correct to me, So here's a screenshot of a typical song with a bunch of typical instruments. 
What I don't see in your shot is why is the instrument track  called Cello? Mine always tells me the name of the VST I'm using. Did you re name those tracks. Could you supply a screen shot and stretch the view out to include all the input and output boxes as shown here. I don't use simple instrument tracks so that might explain why my instruction don't make sense. I use dedicated midi tracks.