I figured that I should post self discovered answers to the questions that I have posed in this thread. Perhaps my ramblings will benefit someone with the same questions.
In a thread about a year old, someone suggested a neat way to handle the torque converter signal that is needed for the PCM. Rather than worrying about wiring a relay, the brake switch from a mid 80's chevy truck with cruise control can send the proper signal. I am going to order one from Autozone and give that a shot.
The fusible links can be replaced with regular fuses or breakers. In past threads, Serehill has suggested these
http://www.delcity.net/store/Auto-Reset ... t/p_198669 rather than fuses or new fusible links. Would 30 or 40 Amps suffice? Do I need one of these for the battery to starter wire too?
I can't find the male to male adapter for the VSS that csuengr mentioned anywhere. Instead, I ordered a new VSS connector and will splice into the green and purple wires. Should give me enough leash to reach the transfer case VSS.
I sent my PCM to Brendan today for programming. My tire size decision had been the delay and I finally picked 31's. The ones that are on the truck now are 29.5 in and I don't think they look lost in the wheel wells.