Okay Chevy (hope you own a nice OLD one), first I am astonished that you use notes below E1. I think ample guitar just used the standard bass tuning, i.e. the lowest string is E1. I know that some people tune their guitars in unusal ways, but I had never heard that of basses. Even 6 string basses have usually the lowest string tuned to E1. But beware, I do not want to offend you in any kind, it is just my experience and I do not have a lot of know-how there!
One thing that is possible with ample basses (and guitars) is that you can tune them other than to 440Hz (in the Settings panel). So I checked that, but unfortunately the maximum down is only 430Hz. If there had been the possibility to tune down a full half tone (you mentioned it above), then you could have done this in combination with transposing the MIDI one half tone up.
To me it seems the only solution using ample bass for your needs, is to transpose the bass line a half tone up and then consolidate it to audio that is shifted one half tone down with Melodyne. But of course that would be an odd method!
Another thing I forgot to say concerning shifting the MIDI 50ms ahead: In Sonar I had always to calculate with the tempo (bpm) how many ticks correspond to 50ms (ticks = 50 * tempo * 960 / 60000 (using 960 ticks per quarter note)). Perhaps you or anybody else knows a better way?