Hello Paul,
This is an interesting comparison. Thank you for taking the time to put it all together along with an actual performance as a "control' sample for comparison.
All in all not too bad but here are some things that come to mind:
I agree with you about the Bb sounding the best.
Are you using the expression fader in any of these MIDI rendidtions? I'm hearing some wide dynamic ranges. For volume and timbre I'll start with the Vel X Fade then try to smooth it out with expression.
Have you tried applying a compressor? I realize most Classical composers/arrangers shy away from things like compression, limiters, exciters, delays and multiband processing because they're trying to preserve a "natural" presentation but, when used in moderation, audio processors can work wonders; smoothing out dynamic extremes, bringing voices out of the mix and masking certain flaws that are inherent with sample work.
For very fast passages you can try turning off the release samples or bring the release fader down below 63. The old GUI allowed you to turn release samples on or off on the fly I'm not sure if you can still do that with the newer VI player or VI Pro.
But thanks again for putting all of this together and posting.