Sounds like some coolant is leaking in the combustion chambers while the engine is cooling down. At cold start, there will be some coolant in the combustion chamber causing some rough idle until you burn it all off. You probably notice some coolant loss after a couple days. I had this same problem for a few months until I decided to get the head gasket done before I warp the head.

 

Hmm, makes sense I suppose, but would a normal compression test be consistent with that theory? I had pressures of about 140 on all 4 cylinders. I thought a bad head gasket would give me poor compression.
Is there any way to verify that it's the head gasket, as opposed to some sensor or the ignition coil or ECM or something like that?

 

Try testing the compression with the engine cold. This is not how you'd normally check compression, but the leak seems to close up when it is hot. The test it not real conclusive. gwl's experience that it is a very slow leak that slowly floods the cylinders while it is off, causing problems on the next start.

The combination of rough running and coolant loss / overheating together strongly implicate the head gasket.

 

My bets are on your head gasket being bad. Your compression can be good even with a bad gasket. I have a very similar problem in my 99 EX (D16Y8). Identical symptoms. Although it sounds like I drive it a little harder then you drive yours. I have a nice symptom where, under heavy load conditions, exhaust gas leaks into the radiator coolant galleys around the cylinders, the pressure builds up and blows all the fluid out of my radiator. Not fun...

You can try a leak down test, they are about $40 and pretty easy to do. Google it and read about it. Although a leak down is usually for testing valves and rings. But if the head gasket is messed up enough it might show in the test.

Changing the head gasket is not worth it unless you can Do It Yourself. A mechanic will charge you the cost of a new block to replace the head gasket. Bare bones you can do it yourself for $40-60 for the head gasket, $80 head resurfaced, $100 for head studs. But your manual will tell you to change any other rubber gaskets (valve cover, any o-rings, cam seal, etc...), and you should follow whatever the manual says you should do, so add another $50 to all that for other gaskets. Have a machinist check the tolerances on the block as well (they should do that for free...). The cost might not be so bad, I am building a B18C, your D16 will be slightly less complicated, and should cost less. Not sure if you have to remove the cam to get at the head studs, my guess is no you don't, but you might have to remove the valve train, so the cam probably has to come out.

The leak may close, but if you get up on the motor, like take it up to the mountains and put the motor under load, chances are exhaust gas will seep past, and you'll get some radiator geyser action like I do.

If your in So. Cal. I know a good machine shop. Let us know what you find out