I'm in the same situation, well almost. My 2001 left me stranded, luckily at a gas station near work. Security light had been flashing nonstop. Figured after a few hours it was the Passlock system and had her towed home (free thru insurance). Then ordered the ignition cylinder and the sensor housing. Got it installed and nothing. Damn thing doesn't go into relearn mode....whether I wait 10mins, 30mins, or an hour the light doesn't stop blinking. It's so damn frustrating to me.
I removed the aftermarket bypass for the remote start and pretty much started from scratch. Nothing's worked. I at one point last night smacked the BCM with the back of my hand and all the dash lights I usually get at startup came on, I waited 15mins and the security light never turned off or went solid. I cranked it and it turned on and died out a second later as the theft deterrent is supposed to.
So, me and a few of my old car audio installer buddies, including the guy I bought it off of think it's the BCM at this point. Removed it. It looks good, no solder joint breaks, but who knows. I'm going to swap it out anyways.
Tried all the efforts to remove power like remove the battery, put both batt cables together, and to remove the TBC fuse from under the dash. Nothing, I still just get crank but immediate shut off. I'm only $75 into it with parts. I ordered a BCM that should be here Tuesday from Amazon, it was $120. There were cheaper with a core return that would have been like $77, but it would be a week before it arrives. I'll update y'all then.