Replaced valve cover gaskets now rough idle

I replaced my valve cover gaskets on my 2001 xterra v6 over the weekend. Had to remove the upper intake manifold as well to get to the driver side valve cover. I replaced the spark plugs while I was at it.
Started it up and it was fine. Two days later it has a rough idle at stops and in reverse. I replaced the upper intake manifold gasket when I removed it. I did not replace the what seemed to be one time use manifold bolts. Some of the hoses were cracked but I didn't break any of them to remove parts.
I want to say its a vaccum leak but from where? Would not replacing the manifold bolts cause this?
Any ideas on what it might be?

Check the Throttle Body to Upper intake bolts.

Are there any cracks in the intake tube?

Are there any unconnected vacuum lines?

Alright I got back early and went to go look at the xterra.
Didn't get a chance to try the brake cleaner idea because as it was running I would heard an intermitant(sp) click. Not the a/c clutch. It would do it more when in drive or reverse with the a/c on then sitting in park. I would say 2-5 clicks a minute in park and 5-10 in drive or reverse with a/c on.
Didn't want to spray anything extremely flamable with a click going on haha.

I think its the #6 spark plug wire. I think something is taking the spark from the wire and its not hitting the spark plug.
I disconnected #6 to see if the click would happen and make the car act like it would try to stall more and didn't hear anything.

What is your take on this?

I'm going to go to the dealer tomorrow to see if I can pick up just the #6 wire rather the spend 40 bucks for all 6 at autozone.
The engine shakes everytime that click happens so I know its misfiring.

I also moved around all the wires cleaned out all the ports on the pass side with an air gun just in case a piece of metal shaving or something was touching it. Didn't touch the driver side because they are all a bitch to get too.
If its that #6 I don't need to remove the upper intake to replace that wire do I? Its a royal bitch to get too.

If you removed the #6 spark plug wire and the idle did not change then your problem is definately in that area, but not Necessarily the wire. I installed a new spark plug a few years back that was defective. You are probably right that it is the cable though.