To allay some of your fears (if any, at this point) I spent a few days riding around the greater Carlisle area in Tom Marantz's JPS 2.5 Suby Coupe a couple of years ago and here are my impressions:
1. It accelerates like a bat outa hell with the widest torque curve I've felt in a looooong time. It is non-turbo'd, fuel injected but you'd never know it - It just keeps on pulling, seemingly forever and launches onto interstates like a rocket.
2. It had a rear-end Suby powering a Suby 5 or 6 speed (can't remember) transaxle with the Aussie flipped ring and pinion. While I found the transaxle noise a bit louder than I expected (mostly 2'nd and 3'rd, IIRC ), I also did not find it objectionable and attributed it to only having carpeting and a bulkhead (and maybe a little Dynamat) between us and the transaxle. Full disclosure, I have never driven a Suby manual for comparison, only a couple of automatics. I can't say it was any louder than a beefed-up VW transaxle - Certainly on a par with my VW transaxle when I have the top up and side windows in and the gear whine lost to wind noise in the Summer becomes more prominent. I sure as heck would never hear my Timex ticking in my Speedster unless the engine was not running.
3. When John was building Tom's car, he asked Tom how loud he wanted it and Tom's reply was something like "Well, I wanna be able to hear it!" so he ended up with a loud-ish exhaust system. That, plus the coupe enclosure, made it a bit loud in the cockpit under hard acceleration. Like, Wait til you've finished stomping on it to continue your conversation because you can't hear each other til the engine quiets down loud. Tom loves it, but I think he might also have invested in some Bose noise cancelling buds by now, at least for his wife. My car is not quite as loud (2,110 and a Berg extractor street exhaust) and I have a pair of Ear Peace buds to keep me from going deaf. 'Nuf said.
4. The fit and finish of Tom's car, both inside and out, was superb with really nice paint. I admit to not being a big John Steele fan, but Tom's car was very well executed and he only reported minor things to be sorted after delivery, all of them done by Tom himself (he's a really good wrench). It took longer than expected, but John was having major health issues and Tom, to his credit, gave him lots of slack til he could get back to building it.
5. I did not drive Tom's car (I don't usually ask to drive other people's cars unless it's offered first) but it rode and handled very well, the seats chosen were cheek huggers and comfy all weekend without fatigue and for a weekend with temps in the 90's, the A/C was fabulous and never skipped a beat - Fast and Cold - and the under-dash A/C panel was nicely done (though obviously a "Vintage Air" unit, it still looked like it belonged there).
So that's it. Yes, we've heard of people on here who were not thrilled with their dealings with JPS, but we've also heard of people who got great cars and are pleased with them. Those people were/are very fortunate. The others, not so much, but I've also known people who got problematic Fords, GM's, Chryslers, BMW's (me), Rovers, etc. Sometimes it's a crap shoot when it shouldn't be, but those who win, win big.
You've got a great car. Drive the snot out of it!