Engine misfire? Help please!

My truck is a '99 2.2L 2WD. This morning is started chugging and idling erratically when going up a hill, and has been doing it ever since. I scanned it w/ the OBD2 and it came up with P0300-random/multiple misfire. I checked all the plugs and the #3 cylinder seemed a bit wet. There is also a horrible clunking noise that seems to be coming from the valve cover. The engine vibrates more with all this going on, and it appears there is now an exhaust leak somewhere in the manifold. If I start it an let it idle it seems to misfire on pretty much every cycle. However, if I rev it up and hold it for a bit the misfire seems to go away and it holds RPMs more smoothly, then let it idle down and it's fine for about 15 seconds then misfires again. I have no idea what is going on with this. I'm hoping it isn't broken valves, or blown head gasket. Anyone who can help, I'd really appreciate it. Thank you.
:banghead:

have you checked to see if you have compression in the cylinders?

I have not done a compression check yet, as I do not have a tester here.

I just drove the truck though about 8 miles round trip. The first 6 it chugged sputtered, and ticked as it misfired. At higher RPMs it smoothed out and barely misfired at all. After about six miles it all went away and it ran normal. Still had a bit more of a tick than before all this, but nothing like it was doing. I scanned it and it showed no codes. I let it idle for about 5 minutes, then shut off and restarted and let idle again. Right now it is acting fine. I'm sure there is still something wrong but I am just baffled right now.

Just a wild guess, but you could have water in the fuel system? I don't think that would cause a long term problem, but maybe for a few miles if the fuel pump picked up a slug of water.

I thought about that, there being water in the tank. It is getting to be winter here and moisture may have accumulated in the tank. I did put in an additive just in case.

What I did was change the plugs back to the old ones I had. That seemed to work b/c the misfire stopped. So I went and bought new plugs and plug wires and installed them. Misfire has stopped, and most of the ticking has gone away. I am hoping that this was in fact the problem and it is now fixed. However, I am still open to any other possible problems you can think of. Thanks guys.

I am woundering about a stuck lifter.
You said you changed the plugs "back", you must have done something before the missfire. mabey you didnt have a wire pushed all the way on to the plug.
If the missfire started, then you changed plugs I mmight be thinking lifter again