Since it happens to both sides and either switch or fob, I'd look at and clean the grounds. G203 is more likely, since G200 is used for so many other circuits (radio, power outlet, cig lighter, GEM, door ajar, etc) you would have noticed problems with.
G203 is located on the DS (looks like) directly under the cab fuse panel, probably under the kick panel. I'd REALLY suspect that ground if your Power Windows are slower than they used to be.
Last suggestion is pull the door panels and remove the connectors from the PDL switches and each door lock actuator. Inspect/clean any corrosion, even put them on and off several times to scrape the connections, if nothing else.
I can e-mail you 2000's schematic, not certain 99 is exactly the same (PM me your e-mail address if you want that).
If that alarm is so new that it caused the PDL problem, I'd take it back to the installer to fix what they caused. If YOU installed the alarm, I'd go back over any connection you made to PDL/alarm.
2000 2.5 MO5D 4.10 one-wheel drive DD - gave to my older son
1990 STX 87 2.9 going in.....Junked it
2000 3.0 4WD M05D 4.10 S-cab Off-Road package with 235-75-15" tires, hotrod DD, lol