I just spent two grand on a full tune up and clutch kit as well as a ton of seals and stuff. the car ran great the first few days I got it back but now I hear air being pulled from somewhere under the hood and the engine acts like it has several fouled plugs. The mechanic put R and R plugs on and other good parts. Is this vacuum related or a dead cylinder?

 

Two grand on a full tune up? Sounds like you got robbed my friend, and from a bad mechanic too.

Well first things first:

Scan for codes

Check your wires

Check fuel pressure

Check that ICM is getting signal to fire

Check opti

 

Check for a vacuum leak.... if you hear air flowing under the hood, track it down. Could be as simple as the intake elbow being torn, or slipping off the throttel body.