I'm like a deer with no eyes when it comes to all of that sorry.
Could you just do what you need manually, like record a usertrack for each chord, using a midi pickup on your guitar also to get the midi.
In realband you can just highlight the bars then go to Generate UserTrack Audio this will bring the picker up, type your required chord in the search box and it will generate the audio chord of your playing in the bar/s.

As you can't make a midi UserTrack "yet" and yes midi is more flexible to work with stretching & transposing, I would use PowerTracks to open the recorded audio with the corresponding midi, SEQ UserTrack, then you simply highlight the chord/s in the chord window then with snapping On drag the midi Track number straight to where you need the chord in realband this will copy just the highlighted midi chord/s.
This way you are not relying on BB to get it right, as you will get it just how you like.
I use this method with UserTracks as BB tends to screw it up transposing other chords too much instead of using the available correct chords.