Erik,
I don't want to complain about your tranny shop since they seem to be working with you quite well, but ...
Maybe they need to think outside the box a little.
There's absolutely no reason that your tranny case couldn't be salvaged if it's just a matter of sealing where the input shaft enters the tranny.
You said that it can't be bored ... but does it really need to be???
That shaft did NOT exit the tranny case without a bushing or a sealed bearing (hardened steel shaft spinning in a cast opening wouldn't last 100 miles). My guess would be that it is a steel clad babbet bushing that is really the damaged part. Unfortunately, there probably isn't a source for an exact replacement. That doesn't mean that you are SOL though. They should be able to find a brass bushing with the correct ID and machine the OD to make it fit. If the bushing requires an oil groove to keep the shaft surface lubricated, then that can be cut with a dremmel.
I'm not just pulling this out of the blue. That's the EXACT same thing I went through on a '87 Samurai I used to have. Granted that we are talking the difference between an automatic and a manual transmission but the input shaft seal doesn't care about that. BTW, I got another 150K miles out of that tranny after my "fix".
Another BTW: The Suzuki shop manual (mine nor the dealer's) even showed that there was a bushing there. The MFR recommended solution was a tranny case replacement. Suzuki wasn't interested in what I proposed to them as the solution since there was already an upgrade to better bearings internal to the tranny that caused the bushing to go bad.