Just went to take a look, to confirm the color codes that Jack was talking about along with reading your post.
If you have the Factory perimeter alarm, that is the door anti theft switch.
If you ground the Dark Green w/ Pink stripe wire to the door latch that will take care alarm issue, but the perimeter alarm will no longer work ( the ground signal to the 97/98 RAP disarms the anti theft module, so even the ign tamper module will no longer work ). This is with a factory perimeter alarm, after market is how ever the system is installed.
The illuminated entry switch shows as a Pink w/ Light green stripe wire to ground ?? Not too sure what this is, does not show in the 99-03 MY trucks ( could be a MY change over in GEM function, as those are 2 different series of GEMs ).
The GEM input for the door ajar switches are L: Black w/ Yellow stripe wire & R: Black w/ Pink stripe wire.