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1.  Thanks for saving a rare and wonderful vehicle.  You know the previous owner neglected the vehicle, it's going to need substantial repair and preventative maintenance to set it right. 2.  I had a '93 3.4L with blown head gaskets.  One head gasket actually failed and leaked, when I pulled the other head I found identical damage in the identical place--it just hadn't started leaking yet.  It's as if there's a "soft spot" in the head casting; the head distorts, loses gasket-clamping in a certain area (near #1, kinda towards the lower part of 1 and 3; and the same spot on #6, towards the lower area of #6 and #4.  Very near a coolant hole in the gasket, and a bigass coolant passage in the block.)  The gasket wiggles free until it fails from fatigue.  Had to mill the heads .015, and I wasn't happy about the wear on the block surface--but I took a chance and it seems to have worked.  Got the engine running beautifully, and then the trans failed.  Haven't driven the car in almost ten years. 3.  Some photos of the two head gaskets stacked on each other, and scarred deck surface attached. 4.  It's two steps away from hopeless, trying to diagnose driveability issues without a scan tool to give you insight into the sensor readings, and the computer outputs.  Sure, codes can be helpful, but the data stream is ESSENTIAL. 5.  It's probably worth your time to conduct a compression test, and then a cylinder leakdown test of the best and worst cylinders, if not all six.  Do this BEFORE you take things apart. 6.  Stay with the OEM-temperature thermostat, and don't bother drilling any holes.  The vehicle has bleeder screws to bleed air from the cooling system, the thermostat doesn't need to pass air when closed. 7.  Plenum gaskets are one thing.  The actual lower intake gaskets--where the intake meets the head--are a known trouble area leading to unstable idle and off-idle problems. 8.  Don't forget about the timing belt.  Previous owner almost certainly neglected it.

Alright, still having issues.  I can get it to reprogram so it only blows out of the upper vents.  I used to be able to get it to work temporarily after resetting, but can't get it to anymore.  I tried two other units that I got from the junkyard and they're both doing the same thing.  What am I missing?  I tested the vacuum system when I started trying to figure all this out.  And now the compressor clutch won't engage.  Maybe I'm low on freon again, but I couldn't find any dye.  I'll have to take it back to my dad's shop again to check the pressures.  I'm beyond frustrated. 

If you got enough turns in to get it halfway I’d say drive it.  Hope you smeared some anti seize on em though or they’ll be a bugger later.

If I understand your post correctly it overheats briefly then is fine if you keep driving it?  I’m not quite sure what you mean by pulling off without letting it get to operating temp. -Have you tried bleeding the air out? Your lq1 can’t do this on its own.  That’s an easy win for sure. There’s two brass air bleed screws up top, 8mm I think, they break easy so be gentle.  Turn them out and bring up the rpm with the throttle body and when it starts to piss a steady stream tighten it up. Do the heater core last as it’s higher up. -Did you do a complete flush and fill when you did the intake gaskets? -if somebody before you mixed coolant types incorrectly it can gum up the rad quickly. Hopefully not as the heater core will be clogged first and that would be  a bitch.   Your issue doesn’t sound too severe so could just be a lack of maintenance from the previous owner.  Like Chris said, water pump or Tstat if the simple things don’t help.

I guess may as well do the thermostat first as its relatively easy. Unless you're getting the fan turn on times adjusted for a lower temp thermostat there is no point. Maybe put a tiny hole in the flange of the thermostat to assist with air bleeding. Even my z34 with a chip in it I have the factory 195* thermostat yet, but have the fans adjusted to keep it more consistent.