I'm glad the 2000 went well, and some are perfect. The PCM setup is the biggest factor in most swaps.
As far as the bypass idea in theory your turning it into more of a BOV setup. Since its vaccuum controlled. And beleive it or not works quite well, with little to no adverse effects. If it isn't setup correctly-then very bad things can happen-like making a call to Ed Morad (not that thats a bad thing :P ).
And its pointless to edit my previous post since you quoted me
However the thread starter needs to find someone with a PT/HPT close by to do the PCM work and scan/tune the car. It gets quite costly very quick sending a PCM back/forth. Try the vin tweaking..that should do it.