05 mustang r/s issues

Well I took out the Prestige APS 920 and put in the Viper 5901. He is putting the Prestige on his other car. I didn't unhook the bypass. I am sure i have the bypass hooked up properly now.  This is what is going on:  There is no power on the green and violet wire coming from the alarm when the r/s sequence starts up the "lock" symbol in the dash flashes (PKALL bypass not programmed yet). On the PKALL I have the red wire to 12 volts, and the black grounded. On the other harness, I have Purlple White to pin 4, and Yellow Blk to pin 3, blue white from alarm is going to ground while running (blue wire from the r/s plug) and Pink going to the pink ignition from the r/s plug). Do I need to completely take out the bypass for the starter wires to see 12volts during R/S? When I start the car normally and then use the r/s and remove the key, the alarm takes over and it stays running. An easy car has become a nightmare but I'm sure it is something simple that I'm overlooking since I'm not longer and installer working on cars everyday.  Thanks

I am having a similar issue with my F150 right now using my PKALL (minus the 10 sec shut down), but you meantioned you put PURPLE / white to pin 3 on your cars wiring harness for it's immobilizer.   Pin 3 is Transmit but PURPLE / white is Receive.   Pin 4 is RX and you have yellow/black (TX) hooked to it... Is that the correct way to wire it... or should it be RX to RX?  Does anybody know?

Its a V8, 2000 F-150

Thanks

Read my other post, Topic:

pkall immobilizer bypass data wires

it has more details of where i am at... Thanks!