46callaway-
You can reuse the stock IMRC controller and leave it mounted where it is now. No need to change anything about that. When you take everything apart, you will need to detach the cables from the cams on the end of each IMRC to make it possible to remove them. While they're out, I recommend strongly that you clean them thoroughly as there will be a pretty thick coat of carbon grime, especially in the secondary runner.
You can reuse the stock fuel rails but be aware that you will not be able to install the EGR valve. I purchased and used an EGR block off plate from UPR products. The pressure regulator on that side of the engine will pretty much rub up against the EGR "ear" on the Cobra upper manifold. I used a pipe cap to seal off the end of the EGR tube, though you may want to either clamp and braze it shut or remove it from the exhaust manifold altogether and cap it down there.
As for the throttle cable bracket, I basically modified the stock one to work and have left it like that. It's pretty much impossible to describe in words how to modify it.
I did reuse the stock TPS and IAC. You'll be using your stock throttle body, just flipped over. The IAC will bolt right on as well, though I experienced an RPM surge at startup that Lonnie was able to somewhat tune out...he said that a Cobra IAC is slightly different and would be another cure for that issue.
PM me your email address and I'll shoot you some pictures of the bracket, hose routing, etc. etc. I wrote up a pretty long post on the "other" forum and will send that in the email as well.
-Dom