Well I think you have a task cut out for you and the Ford manual I have is not that clear, accurate or easy to plow thru'. But here goes:
From what I see the central timer module accepts separate inputs from 4 sources relevant to your mod; front door handle switches, driver's door jamb swich, the three other door jamb swiches and the factory remote entry module. I presume the driver's door is kept separate so the timer's logic can activate other functions such as headlight chimes, key-in buzzer, etc. The remote is kept separate since it always requires a delay (to keep interior lit as you approach, and unfortunately, to your chagrin as you walk away). I don't understand the separation of the others (although inside timer they may all come together), but backfeed of 12+ power may be the reason.
The timer controls lights via courtesy light relay r12 which is white and should show in your owner's manual (located top left of interior fuse panel). This relay has its coil energized from the timer and the relay's contacts close to complete the ground path for all lights; domes, under dash, under door. The timer logic decides whether to allow r12 to be energized, and when to de-energize it, with/without delay.
If you simply remove the above inputs from the timer and rewire r12's coil circuit to accept them as inputs you will lose driver's door functions from the timer as descibed above and perhaps others I'm unaware of.
Digest and critique the above and I will tabulate pin-out for timer in a subsequent post.
