98 Explorer PATS problem

Last week I installed a prostart remote starter/keyless entry system in my 98 Explorer,after all wiring was complete I tested the system (with my key in the ignition to allow the anti theft system to think it was being starter by the key).Everything worked fine so I was ready to install the PKF bypass.I found a four wire connector on the steering colum but unsure if it was the right one so I disconnected the plug and tried starting with my key,it did not start and the theft light blinked rapidly so I knew I had the right plug.I proceded to cut the one wire and splice into the other wires according to the PKF drawing,however when I was ready to program the PKF it would not let me, every time I put in my key the theft light blinked rapidly. I removed the PKF and reatatched the wire that I cut but still none of my keys worked.Called Ford they said the PATS system would have to be reprogrammed by them so I towed the vehicle in ,they tried to reprogram but could not so they did a system check and found that there was power going to the PATS module(located behind pass. air bag)but no power comming out ?... They said I needed a new PATS module so I said go ahead and fix it .I picked up the truck the next day, I tried it in their parking lot it started fine the first 4 times then the 5th time it took quite a while to start almost as if it was flooded.They said it was fine and I went home.after I shut it off I retried it and it would not start (theft light blinking)....called Ford they said to remove steering colum cover and wiggle the wire to the ignition ,well bingo that was the problem,it sarted up so here is my question:did I F....  up the PATS module when installing the bypass or did I just pull on the wire to the ignition causing it to become loose or both?has any one ever damaged an antitheft system when installing a bypass?this cost me almost $400 to repair so far.This angers me because Ford knew there was a wire loose in the ignition yet they did not fix it and how do I know if they actually replaced the PATS module like they said they did?.

when I tested the wires for the bypass install I used a digital multi-meter,in the bypass instrucions it says to use a logic probe,not sure what a logic probe is,could my multi-meter have caused a problem?.I am pretty sure I installed the bypass correctly but If I did have the wires mixed would that damage the PATS system?

I would really like to have this remote starter working but Im afraid to try anything untill I know for sure.

The pkf does not list as working for the 98 explorer.

I cooked a 99 with a pkf, and have never used another one.

When I was a nOOb I stripped all the ( vehicle) wires at once, and was connting the pkf wires, shorted two out together, and the truck never started again. 6 bills latter.

I guess that's the price of doing it yourself.

that 200 $ dollar install ( with warrenty!) is looking pretty good right about now, eh ?

Well I went back to the Ford dealer today to get an 8" scratch water sanded and buffed out of my door that they put there when repairing the anti theft system (ya, i've had a bad couple of days!) any how I asked to see the module they replaced but they could not find it ,Im pretty sure they did'nt even replace it . They probably just found the loose connection on the ignition and pushed it back into place.I must have pulled it when splicing the wires?.Thanks for all your replies!.