Sorry, been working, between that and the "reply" window often not showing up... anyway, as I said earlier, I do find that option available, but I haven't found it already "checked", and in every case so far it is greyed out in the "unchecked" position.

Ah sorry, I missed that part in your previous reply :)

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I can see one of your problems is in the synth rack.. You only need one instance of TTS.
TTS-1 is a 16 channel synth. Having more than one inserted will cause confusion. 
You can quickly see which synths are being used buy checking the SOLO button in the synth rack. Delete all unneeded synths. 
 
And when you click on the INSTRUMENT ICON ( looks like a keyboard)  to the left in the track inspector to open the GUI the synth that opens is the synth that is assined to that instrument track. 
What I see is you clicked on track 13 and TTS-1 opens, correct? 
 
If I was you I would abandon using INSTRUMENT tracks and use a MIDI track. This is a classic case of why you shouldn't use instrument tracks. 
 
INSERT A MIDI TRACK above or below  each instrument track
Drag the midi from the instrument track to the midi track. Be careful not to shift in time. zoom in a bit. 
Now set the output of the midi track to the instrument VST you want to use. 

Again, that's not something I "did"... there are still several tracks that I created with a VST Instruments that for some reason defaulted to TTS-1.
 
Correct, I clicked on the Instrument icon and the TTS-1 opened, but it should not, it should be the Rapture Session GUI.
 
As regards creating a new midi track and transfer the midi info.. I have done that, but once I save the project and close out, then come back in, it defaults to the TTS-1... at least that's been my experience the last couple of weeks, I'll try again, when I get home.
 
I'll think about all this moving forward, I'm trying to save this song and mix this piece... I still don't know why I'm hearing the wrong instrument on a track in solo.
 
Please remember, I'm not really trying to learn a new way to do this, although I will pay attention to the tips moving forward... I'm trying to save this song so I can mix it asap.

I don't know if this is related to your problem, but as a beta tester I did once report a bug in which deleting a synth from the synth rack that had MIDI-output enabled causes the routing of other MIDI tracks to get screwed up. Are you sure that you didn't remove a synth that had MIDI-output enabled? Here is the bug recipe:
 
Steps: 
1) Insert a MIDI track
2) Insert a synth into the rack with MIDI-output enabled
3) Set the input of the MIDI track to this synth
4) Insert another synth into the rack with MIDI-output enabled
5) Delete this new synth

Expected Results: 

After deleting the 2nd synth, the input of the MIDI track should remain set to the first synth. 


Actual Results: 

The input of the MIDI track changes to the previous synth in the MIDI input list (if one exists), or to Omni (if no other synth is in the list). 

Again, that's not something I "did"... there are still several tracks that I created with a VST Instruments that for some reason defaulted to TTS-1.
 
Sorry but it is something you did. You are Not following my instructions and not trying to learn how it works. This is as far as I can go until you follow the simple instructions. 
 
Please remember, I'm not really trying to learn a new way to do this
 
So therefore you can continue to do it your way and it won't work and you can blame the software when this is a simple matter of not learning how it works. Why do thousands of people use Sonar without this issue? They learn how it works. It's a learning curve with a steep slope if your new to the world of midi. You'll get it, but it takes time and effort on your behalf. 

I don't think I did, but assuming I did, how do I fix the remaining tracks so they are playing the correct instruments? And it looks like it's correct, that if I delete a midi track, everything else gets shifted... this hasn't been happening for the last several years I've been using Sonar, what changed and how do I fix that?

Not an answer to "what the heck caused this"...and as I mentioned earlier for me it came about suddenly around the time Windows updated on my computer end of last year. Random older projects that had been fine with functioning midi tracks no longer playing back.  As a work around I've inserted new soft synths (insert > soft synth) and had Sonar create the necessary tracks, and selected the same synth that won't play on the previously recorded midi track.  Than I just drag copied the old midi track to the new empty track and its been working

I'm sorry but windows has absolutely no bearing on changing Sonar midi tracks around. That's more or less impossible.  
 
Because of the many threads asking for help with midi I'm going to start a thread with clear instructions with screen shots on a step by step process from start to finish of how to set up a project and play midi. This information is already very clear and in detail in the help files, but it would seem people prefer to not read those. So I will post this when I get a chance. I have all the screen shots, just have to upload them to Imgur.