Chrysler Repair: 96 Chrysler Cirrus, Random Misfires, Rough Ride, chrysler cirrus, upper intake manifold

Question
I AM IN SERIOUS NEED OF ADVICE WHEN DEALING WITH MY CAR DEALERSHIP SERVICE SHOP!

I've not been too proactive with regular servicing (aside from oil changes/brakes) so I took my car in for the 120K works.  I had the following done:
Fuel Injector Flush
Throttle Body Cleaning
Transmission Tune-up
Oil Change / Filter Change
Brake Inspection
Engine Tune-up
I was also having some mild problems with the car riding a bit rough once warmed up.  It would run rough in patches while driving and while idle.  They came back to me telling me I needed the valve cover gaskets replaced (I fear grossly overcharging me - he originally quoted $710 to replace the gaskets causing me to blow a gasket of my own.  He then lowered it to $350 which I think is probably still too much but what do I know).

Here are the technician notes from the engine tune-up:
TECHNICIAN PERFORMED ENGINE TUNE-UP.  CONNECTED DBR TO PCM, FOUND FAULT STORED IN SSYTEM P0303-P0300-ENGINE MISFIRE DETECTED.  REMOVED UPPER INTAKE MANIFOLD, REMOVED SPARK PLUGS, FOUND OIL SEAPING FROM VALVE COVERS ONTO SPARK PLUGS CAUSING THEM TO FOUL.  REMOVED AND REPLACED VALVE COVER GASKETS AND SPARK PLUG TUBE SEALS.  REPLACED SPARK PLUGS AND WIRES.  RE-INSTALLED INTAKE MANIFOLD AND NEW GASKET.  CLEARED.

Well as soon as the car warmed up I had the same rough ride problems when the car was ran idle - it had stopped doing it while I drove however.  That was until about 25 miles later when the Check Engine light started glowing and it now runs rougher than it did before I took it in there.

I've been reading answers on this site and see that P0300 is not associated with a particualr cylinder, rather random misfires.  Are there things that would normally be checked in the course of all my services listed above that I can question them on?

PLEASE do you have any advice about how to handle the dealership?  I have to take it back in now and I'm scared.

Answer
If they said the miss fire was from the plug seals leaking into the chamber and they repaired that and it did not take care of it  go back in be firm and say that u told me that it was this and it did not correct the issue that i paid for I would like for u to check it out and tell me what is really wrong. Talk to the service manager  be nice at first and if u dont get it at least looked at then time to get a little mean about it ya know?