For Q#2;
Amp simulators are intended for DI recorded instruments such as a guitar recorded directly to the track with no amp or microphone. But's since this is art feel free to convert your midi tracks to audio and try some amp simulators on it. The results may not be what you want but will surely be unique.
You can put your midi guitar solo on BIABs Melody track. You won't be able to experiment with RealTrack "sounds" because RealTracks are not midi samples.

However, you can easily change the midi instrument by right clicking on the Melody track and use the dropdown box/es to choose GM/GM2/other midi voices. I, myself have not had great success at getting IK Multimedia SampleTank to function within BIAB. But, it works fine in Reaper DAW ($60)
I think what most of us do is punch out the chords how we want them in BIAB, choose a few styles that we think fit well, then move the individual audio and midi tracks to a DAW to do the things you are looking to do.

If you just want to import stems to remix you should do that in a DAW like RealBand that come with BIAB. Import each stem onto it's own track, then remix. Hopefully your stems are .wav and raw with no FX. If your original tracks you recorded elsewhere have a click track or midi drum track you should import that also. That way when you change tempo or stretch timing you can include the tempo track to help keep all in sinc.

What did you originally record your songs on? The VS workstation... is that a hardware digital recorder? Like an old Mini Disc multitrack recorder? Can you connect it to your computer via USB, Optical LightPipe, or a multi pin interface that was made for it? If so, you might be able to dump your tracks directly to your computer without the wait time to do each track one at a time.

Q#3; What are "reference" tracks?

Does the noise in your head bother me ?