Anthony,
The idle speed is electronically controlled. There should be a trim plug somewhere on the car, numbered 1 through 7 (round knob). Pull it out, turn to 1, push in. Idle speed should drop to ~500. Pull out, turn to 7, push in. Idle speed should increase to 700+. If not, your ELR circuit is not working, and your car is idling at the pump's mechanical minimum idle (which it isn't supposed to). Idle speed should be something like 630rpm, I think. To test the ELR actuator on the pump, remove the connector, and BRIEFLY (like one second tops) apply 12 volts to the two terminals. Idle speed should jump up. If not, the actuator is probably bad. If it does, the signal to the actuator isn't getting through. My car had a broken wire at the connector, a quick re-solder job fixed that.
Rough idle problem: I would start with a Lubra Moly Diesel Purge treatment first, if the car has never had one. If that doesn't help, I'd pull all 6 injectors and have a diesel shop pop test them. If they're all OK (good spray pattern, etc) then the problem may be in the pump - delivery valve seal leaking or something like that. Last item is motor mounts (or first item, I guess). They don't often last more than 50-75kmi, so if they're not pretty recent, inspect them closely. The hydraulic type (round saucers) collapse and don't isolate vibration anymore, while looking fine externally. And yes, 1.0 ohms per glow plug means they're fine.
As to setting idle speed, injection timing, and anything else - you need the factory service manual. Myself (and others here) won't repeat the procedures for you. We'll help you if you don't understand them though.
Either get the printed manuals off eBay, or get the CD-ROM (dealer or eBay).
HTH,