Don't worry about the MAT, it doesn't effect performance. The hotairs didn't come with that sensor so if you didn't add one when you did the ECM conversion, it's not there.
I'm trying to think of everything you had to disassemble to install the kit. Does the intercooler piping come close to the coilpack at all? I had a plug wire that would arc to my IC piping on the Spearco kit, couldn't find the problem until I popped the hood at night. Since the compressor housing on the 49 has been rotated differently than on the IC cars, are all the bolts for the compressor housing there? At least one of them goes through and will cause a vacuum leak if missing. Why was turbo link locking up? What else did you do besides install the kit? It could be so many things. Is the alternator putting out like it should, plugs gapped too wide, bad wires, coilpack or ECM not grounded properly, intake leak, bad MAF, etc.
The best way I can think of to test an intake leak on your setup is to have someone stall it up with the hood up and stand beside the car and listen for leaks when it hits boost.