Hi Ian!
Always hard to "lose a friend" in selling a bicycle (one reason why I've not been able to part with one since childhood), but the good news is this opens opportunities for a future ride that better suits your needs. It also made Thomas very, very happy and it is nice to bring a bit of joy to the lives of others. Though you may not be on your beloved RT, you'll still be cycling and that's a wonderful thing.
I can address a few of the points you mention...
I ran 26x2.0 (actually 47mm inflated to my needs) Duremes on my Mk2 Sherpa and as I recall I did indeed have to deflate the tire to clear the front pads. I believe the fork on the Mk3 Sherpas may be marginally wider, so perhaps this would not be an issue on the current frames. Best to check with SJSC/Thorn to be sure. Do you have to frequently remove the front wheel? If not, I found I only had to let out a bit of air to clear, and didn't have to pump it back up from flat.
Andre is far more expert in this realm than I, but I wonder if it might be possible to employ an 8- or 11-speed Nexus/Alfine hub with your BB-mounted motor and come out with a pretty ideal motorized IGH setup. Certainly, there have now been a couple very nice Sherpa-to-Rohloff conversions and this would not be so different. The bike even includes a derailleur hanger in the event a chain tensioner is needed. Of course, there's always the option to go with derailleur gears, and this is not a bad thing by any means.
There is one other possibility I'll toss out there for consideration, Ian. Given Andre's success with an open frame, might one also be worthy of consideration for this application? Looking to the future, it would make mounting and dismounting even easier than the Sherpa's sloping top tube and if one isn't planning to carry heavy touring loads, there aren't (m)any disadvantages.
Please keep us posted as things move toward a decision. Know good wishes go with you for finding the perfect combination for your needs.
All the best,
Dan.