Bryan
A few points here:
1. I have a John Craig TA49 and I think it's terrific. If you do a search you'll soon see that John Craig is probably the most reputable turbo guy we have. I think you'll be satisfied.
2. When I got my turbo from him, I had to return my stock one also as a core. I paid a little more for the TA49 from him (including considering the core return), but hey, you have to pay for the "best".
3. As for your combo, everything looks good except your injectors may be a bit small when the TA49 is working it's hardest. For comparison, I have 009s (42.5#). For street driving, your 36#ers are fine. On the street, you'll probably notice no difference between the stock turbo and the TA49 unless your stock turbo was a POS and in that case you'll notice a big difference just going to any new turbo. It's at the track at 25 psi boost where you'll see the TA49 helping you make 50 or so more HP over the stocker.
4. Don't know anything about this adapter you're talking about. Maybe others have heard of it, but I haven't. What is it? If you're concerned about what John will give you in exchange, just ask him. Or maybe just don't get one from him, keep yours, and get it ported appropriately (whatever that may mean).
5. What does it mean when you say...
I just had major work done by a very professional mech and need a new turbo.
Almost sounds like your mechanic messed up your turbo!
Mike