item 1 - if the fan is running direct, how did you make it auto again? its a 2 speed system that is controlled by a temperature module. If you fiddle with the temp sender it will make the engine think its running cold and operate the glowplugs too while running. Or were the relays just bridged?
for the heater - remove the glow bus bar and check each plug with a multimeter for resistance. it should be about 1 ohm per plug (for a 11V plug) and how or why is it shorting in the first place, you wouldve blown the glow fuse from that short. Check the entire wiring for open insulation and touching to ground and repair as necessary.
The glow system applies voltage to the plugs once when the ignition is switched on, keeps it live while cranking and keeps them running for 10 more seconds - and switches them on and off during cold operation. Once hot it goes silent.
for vibration check the mounts first, and for nozzle spray, check each injector noise for similarity with a stethescope or rubber pipe (they should sound clacky like a metal valve hitting solidly) if they sound different then you have (bad injector/bad delivery valve on pump) - Buy some diesel purge, mix with equal fuel and feed it to the engine directly - both in and out pipes should be in the feeding bottle - it will clear out the pump parts and nozzles too; you will feel it run smoother as you do it - feed it till it nearly empties the bottle, (you dont want it to suck air) - connect the original tank lines and you are good to go. For nozzle spray pattern check you would need to take them off the engine and check them at a diesel lab with a spray tester, they should spray conically and should pop (start to spray) at the pressure stamped on the nozzle holder, and they should make a sharp creaking sound when operated with little strokes, do not test them like they are continous spray nozzles. They should also not leak at about 90% rated pressure - forming of a drop of diesel at the tip at 90% pressure is acceptable
