I have been having problems with Sonar talking consistently to my AKAI MPK261, so I don't know if it's related, but I updated to the Windows 10 Creator's Update and afterward could not get them to talk at all. I tried going over all the midi and device settings, and as far as I can tell they look right, or least the same as before, but now I have recorded midi tracks playing the wrong instrument, and still cannot get a conversation going between Sonar and the AKAI... any help would be greatly appreciated.

It's like the tracks are shifted... I'm hearing both bass parts if I solo one of the bass tracks and the string track. Really confused here, any help would be appreciated... I'm still playing with settings and getting some results, but now it's even more weird. I have a bass track and a string track, both midi, I can see the recorded information... (the bass is made up of two actual bass tracks but only one is sounding for some reason, all the settings are identical) but now, when I have the STRING track in solo I'm hearing the BASS part... I can see the recorded info on the track is correct for the string part, but I'm hearing the bass on that solo'd track... and what's more confusing is, the bass track is dry, but the solo'd part I'm hearing has the reverb assigned to the string track. Something is terribly wonky and I can't figure it out. 

Nobody? Nothing?

Did you update your drivers?
The new windows 10 has the most problems with drivers.
I would check there first.

Hmmm, okay, well, I am generally pretty up to date, there's nothing available in the Command Center, I've updated the Presonus, the midi controller website doesn't offer anything... that being said, I can see that as a reason I'm having trouble getting the controller to talk to Sonar, and I'll keep exploring that, but I'm not sure how that would affect the main issue... I'll try to be more concise, I have two bass parts and two string parts, if I solo the first bass part (track 3), I can see the midi info in the track, but it doesn't play back and the meter isn't reacting. If I solo the second bass part (track 4) I hear the first bass part played back. If I then unsolo the second bass track, and solo the first string track (track 5), I hear the second bass part, even though I'm not soloing that track, and the part is being affected by the reverb on the string track (the bass parts are dry). Each track seems to be shifted down.

Are you using drum maps? 
 
The Sonar update (2017.03) shifted all my drum maps by +1 with similar problems as yours. 
 
Solution was to reselect the original drum map in the drum map manager. 
 
 
 

I'm not knowingly using drum maps, the percussion parts I have on this particular piece, I built manually in the Piano view, if that's tantamount to using drum maps, then yes. However, my issue is with bass and string tracks, which I initially played in from the midi controller as soft synth TTS tracks. I was able to recreate the song in a different file and everything is correct, except I can't seem to punch into the prerecorded midi tracks, I have the correct sounds assigned to them, but my controller still isn't talking to Sonar for some reason.

Hello, 
I ran into the same issue with my saved templates and my updates to Windows 10. It seems to not remember the midi settings and seems to set them based upon either how it picked them up via pnp pecking order or if usb how the controller "ordered" them. I had midi instrument tracks to move with Midi Omni settings all over the place. I was able to look at my older template copies and manually adjust each track to the correct setting. With that said, I found it much easier just to rebuild the template and save. IHTH
 

Interesting. Unfortunately, I'm not all that midi savvy... as I said, I was able to rebuild the piece in another file, and was miraculously able to reassign the same TTS sounds to the imported midi tracks, but I still can't get my AKAI MPK261 to recognize the tracks so I can continue recording, I'll have to either start over completely or build the rest of parts note at a time.

If it is just this one project that is tangled up, I would just create a new project with tracks the way you want them and copy the midi clips into the new project. Not a solution to the problem but might get your project back in order faster than trying to figure out what fouled it up in the first place.