As Markwb suggested, you quite likely are having a problem with air pockets in the cooling system. If all else fails, pull the thermostat again, and dirll a small (1/16 or so) hole in it along the edge. That will help to get rid of the air. Also do what Bill Boost said and keep a close eye on the coolant level.

Here'* a fill method that will minimize the likelihood of air pockets in your engine. If you do this procedure and are still losing coolant after a few days, I would guess you have a perforated UIM or bad LIM gaskets, allowing the coolant to leak into cylinders where it causes rough running and is vaporized out the exhaust. You might be able to detect this type of leak by smelling for coolant at the exhaust pipe.
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This method was developed by trial and error and has been found to be effective to minimize the possibility of trapping air pockets in the L36 3800 engine cooling system. Trapped air could allow for increased temperatures around the hot EGR passage in the plastic upper intake manifold, leading to failure of the manifold, internal coolant leaks, and severe engine damage.

When refilling the engine and radiator with coolant after repair work, remove the radiator cap, then remove the thermostat and drill a small (1/16" - 3/32") bleed hole in the thermostat flange. Check the brass bleeder on the upper radiator hose fitting to make sure it can be opened and closed easily. With the thermostat out, begin filling the engine with coolant at the thermostat housing until the coolant reaches the lip where the thermostat seals. Do not install the thermostat or the upper hose yet. Fill the radiator slowly at the cap opening with coolant. You should see and hear air bubbles disturbing the surface of the coolant in the intake manifold at the thermostat housing as they are pushed up and out of the engine. The coolant level will eventually start to rise in the manifold as the coolant in the radiator gets high enough. Install the drilled thermostat, positioning the bleed hole at the 12 O'Clock position. With the thermostat and upper radiator hose installed, pour additional coolant into the radiator slowly, until it rises to the overflow hole in the radiator neck several times. Allow several minutes each time for the top hose to fill and for air to bleed past the small hole in the thermostat flange. Repeat slowly filling at the radiator until the level in the radiator remains steady for five minutes. Fill the overflow tank two or three inches above the "full hot" mark.

Start the engine and bring it to operating temperature. If possible, take the car for a drive. You will be able to tell when the thermostat opens when the top radiator hose gets hot. With the engine at temperature and idling, open and close the bleeder screw to expel any air. Even if only coolant is expelled when the bleeder is opened, wait a minute or two and try to bleed it a couple more times. Shut off the engine. If the cooling system has no leaks, the level of coolant in the recovery tank will drop as the system pulls in coolant to make up for displaced air and thermal contraction. Bring the level in the recovery tank back up to "full cold" if needed and observe the level daily until it stabilizes.

Original water pump as far as I know. I'm the 2nd owner.

Coolant doesn't spew anywhere. Level is stabilized as well now. Seems to be all fixed

Glad to hear you were only a vicitim of the air pocket... I think we've all had an air pocket at one time or another.

glad to here it wasnt your water pump! god i hate thos things

Update / also in original post:
SON OF A @#$@#$^@#$

So I get the vacuum line hooked back up, as below, and everything'* great for 2 weeks.

As I'm driving home from a friend'* house on Sunday evening, about 2 blocks away from my house, I start getting the shudder problem again. I think oh ****, what now. Pull in the driveway and park it (it'* almost midnight).

I look at it in the morning, and it'll fire, then die right away, like I turned it off.

I get the mechanic out today, and he puts a scanner on it. Scanner isn't reporting any codes, but the voltages coming back are wrong (reference 5V line coming back at 6.62V), and it looks like the injectors are pumping out full blast at start, and flooding the engine.

So, unless anyone has any suggestions (which I will GLADLY take), it looks like I need a new computer (PCM?). What'* involved in swapping this? I've searched for a few threads, but haven't come across any detailed stuff.

Any advice is gladly appreciated.

while the PCm'* (computer) do go bad from time to time.. I'm wondering if there'* another issue. When the mechanic scanned it..did he say if all the other items like Maf and IAC looked right?

Mechanic said the computer was sending back all kinds of wierd information, so he doesn't know what to trust. I'll ask him today exactly again. It sounded like it wasn't throwing any codes, but the voltages being reported were far out of spec.

From my searching on the board, it looks like if I replace the PCM, I need to pull the EEPROM chip from my old PCM and put it in the new one?

FWIW, I traced out the wiring that I could, and didn't find any melted insulation that would cause a short. I also tried unplugging the MAF in case the new one was causing a problem, but that didn't fix it either.