The low side port should be on the passenger's side of the engine, sticking out of the large cannister-looking thing (at least it is on my '92). For best results, you should be using a manifold gauge to add refrigerant to your system; however, if you don't, make sure you add small amounts at a time and let the unit pull down, checking the performance of your system (ie: vent temp). As for the service cap, it's for both keeping debris out and preventing leaks through the schrader valve, but as long as it is not leaking out at the moment, it should be fine (off cycle pressures can be around the 100psi+ range; wrapping electrical tape around it will have NO effect). You can check to see if it is leaking by applying some soap & water solution to the schrader valve and see if it bubbles (PLEASE make sure you either do this after adding your refrigerant or completely dry the water off the valve; trust me, you don't want water inside your system!). Then later on you can scrounge around the bone yards to scarf a cap (just make sure it's from a R-12 system; the newer 134a units have different sized service ports).

Hope this helped a bit...