need help with programming pcm

[balistic]

in my 96 f350, 460, i pulled the auto and put in a ZF 5 speed. My pcm needs changed or flashed now, its running but has a few issues. I am not sure wich new comp to pick out, and was wondering if the original can be flashed, who can do it (the dealer cant), and what parameters i might be able to have changed, such as, with no clutch safety wiring in the cab, I would need the bypassed so it starts. I am afraid if I just put in a manual trans PCM it won't start due to no clutch safety. Any advise, or any of you do flash/reprogramming???