Whew! OK, let's see:
"I read in my "how to keep your vw alive forever book" that this is caused by a distored flywheel caused by a spring broken on the pressure plate?"
Yes- that can be a cause, but first, look for any oil leakage behind the flywheel that might have been getting onto the clutch plate or disk. If that happens, you'll easily see the stains on the clutch disk (they look black or burnt). If something is leaking (usually the rear main seal or the cam shaft journal plug) then you can easily replace them. Aircooled.net has a nifty tool for inserting the main seal that uses the flywheel gland nut as a press.
If nothing is leaking and you've gone to the trouble of pulling the engine, then a nice Kennedy stage 1 or 2 pressure plate and stock clutch disk are in order. Stay away from the 4-puck clutch disk, as they tend to be binary in application - they're either full on or full off with little in between - great for the Drags, but not cool for stop-N-go traffic.
"I have dismantled much of my engine in hopes of finding something telltale of why im running near 300 deg oil temps on the highways... i think my thermostat flaps were staying closed, tell me, what will i be looking for on this thing after i drop the motor out.. "
How do you know what the temp really is?? The best way I've seen is a dip-stick thermometer (mainelycustombydesign.com). Once you know what the temp really is you can begin to cure it.
Take the vanes out of the shroud and polish up the moving surfaces to make them move freely (steel wool is good). Replace the little keeper springs (they're cheap). Replace the thermostat (it's cheap, too) and adjust per the service manual.
Do you have all of the engine shield sheetmetal installed? It should completely isolate the top of the engine bay from the bottom (hot exhaust) area. If these two areas are not isolated from each other, you'll NEVER get it to run cool.
"Also, the only way i can see of putting my external oil cooler on is to yank my doghouse cooler and put on the adapter for it... should i get a new fan shroud then? Im told pulling the doghouse cooler cools #3 cyl better. true? or should i wait and buy a new oil pump with the in/out lines machined in? "
EVERYTHING I've ever read from Gene Berg and Jake Raby tells me that pulling the doghouse cooler will make #3 cylinder run HOTTER, not cooler. The best way to get a full flow oil cooler installed is to pull the oil pump and plug the output port, then add a full-flow cover with an oil output on it, then drill and tap the end of the oil gallery for the oil return. Look back to my oil cooler project posts for a lot more detail on this.
If you run a pump cover with BOTH input/output fittings, it only skims a portion (might be a SMALL portion) of the total oil flow to go to the external cooler/filter - not cool. Doing a full-flow conversion is a lot of work, but it's the best way to do it.
Gordon