2005 colorado shift interlock

I installed a viper 5902 in a 05 canyon , everything seemed to work correctly till I attempted to go from remote start to key inserted operation. when I press the brake pedal the remote start turns off, (truck stays running) the instrument cluster isnt powered fully, no gauge operation, the accessory / blower is turned off and the shifter is stuck in park. If I turn it off and start it with the key everything is fine. I was reading in a couple of posts about a proper key sequence on these is very important. I am using a bypass module Pk.. something, dont remember, Ill check and post it up if needed. When I first finished the install the truck would not start , It would want to start then shut down quickly. After several tries it did start but I have this shift interlock and accessory problem. Does any one have any suggestions. I didnt use the DirectFax document 1603 to wire in the pass lock. I didnt think I needed to since I had the bypass module.

The only one that I cut was for the pass lock, I think it was WHITE/ blue. all of the other wire connections were just skinned, soldered and taped. I was thinking that there must be an ignition wire needing fed but there are only 2 that i have found need fed. Ignition 1 and accessory. thats why I was thinking it was a sequence thing. Is the BCM going to be looking for the Key in signal? If so I dont see how it can in the current wiring. From what I have been reading the sequence is :key sense, second ign, starter, then passlock resistor. Has anyone ran into this being a critical issue to get everything to work correctly?

The Viper model is a 5901 not 2, and the passlock module is a (XK06) PLXR Platform 06 with 3.0 firmware. On the passlock module, Where should I have hooked up the Brown(-) ground when running, and where on the Orange (+) starter input. Maybe I have these goofed up, I wasnt 100% sure when I hooked them up. I know when I went to program the resistor code with the instructions it wouldnt follow the procedure on the instructions. The truck started so I didnt worry at the time.