Does anybody have any ideas for what is causing my rough idle.

Do you have the oxygen sensor hooked up yet?

Yes and it works great.

(picking at details in your garage entries) EGR is hooked up? The valve is clean and closing properly?
Does it only idle rough when the car is in motion?

When I am driving it doesn't really happen because I get a bit of rev hang at about 1100 rpm. When I stop at a light it will take a few seconds but when it gets to idle it starts running rough. I have the idle at 750 rpm. At stock idle it was too rough. The egr is connected. I cleaned it when I put the motor in in November. That's what puzzles me. The rev hang suggests a vacuum leak. Yet when I connect the timing light it kind of misfires because it won't show the timing marks every few go rounds or it's retarding. But it shouldn't retard with fixed timing. I checked the egr with my vacuum pump also. Also when Ipump my brakes it revs up and down.

I found that I have a misfire in cylinder #1. I thought I would check the timing one last time. I sat the light down and noticed it was skipping every other second or so. I connected the #1 plug wire to the #2 cylinder and vice versa. It then didn't do it on either cylinder as much but still some. The value craft wires were not a good idea. The wire for cylinder 1 is loose and the inside of the hole on the dizzy for cylinder 1 is worn out. WHen I replace the cap and wires I'll give you guys an update. I'm going to the dealer this time.

NGK makes a decent set of wires, though they may only be a few bucks cheaper than the OE sumitomo wires, depending on where you get them.
NGK HE76: ~$46 through amazon
OE Sumitomo: $55-80, depending on dealer

Thanks for the info. That's what i'll get.

I've used Duralast wires for a long time and have never had issue with them. Plug wires is one of those things that spending big money on them doesn't get you much.

I think I paid $16 for the set on the Durango right now.

Meh... I've heard enough horror stories about Autozone brand parts (electrical parts in particular) that I've opted to just avoid them all together.
Besides, the Duralast set is only about $5 cheaper at $39 + $2.34 MD sales tax.