When I start the truck up in the morning or let in sit for about 8 hours, when I I start it up it idles rough then revs up and is steady from there on. And it will only do this if like I said let it sit for a while.
I have:
New plugs
New Wires
Cat back
Headers
180 thermostat
K&N system
new valve cover gaskets
I'm thinking a misfire or something.

An older truck?

It is 2001 ram 1500. with 94K on it. 5spd

I guess it's a gas engine since you mentioned plugs, and headers. Six cylinder?

It's a 318 V-8, fuel injected

AH......have you checked with a dodge dealer as to if the computer has been upgraded? I have a similar problem in my RAM which is also the 5 spd. 5.2L. Mine only shows up real abd during the winter and colder months. BUT I am having ti fixed in a few weeks so I will be set and the problem will be solved. NOTE: By doing the upgrade the shift indicator light will not be functional. My indicator light works that is how I know it has not been upgraded. Here is the link for the TSB on it.
http://dodgeram.info/tsb/2002/18-011-02.htm

I do appreicate the info and will give it a try. My shift light does come on still so my has not been flashed either.
THANKS