What would cause my 2000 ford ranger to run rough at a cold?

I have a 2000 ford ranger 4.0 motor. I've changed the MAF sensor, put fuel injector cleaner in it, and replaced the fuel pump. When the truck sits for awhile this pain runs rough for about 30 seconds. I did not find any air leaks or a crack in any air line. The only info I can tell you is there's a chirp between the motor and transmission. Also that when you disconnect a spark plug wire from the coil pack and set it off to the side sparks are still shooting out from the coil pack. Only in that one spot though so it's magically finding a ground outside of the coil pack. This truck is supposed to have the 3.0 and has a super chip. I'm just trying to find out why it runs so rough at a cold start

Well if sparks are shooting out of the electronic distributor, then that might be your problem. Try checing your spark plugs and wires.
How to Check Spark Plug Wires

Do you have any check engine lights? Have you tested your fuel pressure?
Fuel Pressure Test

I would also double check for any vacuum leaks. They can be small and hard to find.
You might want to check the IAC and clean it. That regulates the amount of air coming into your engine at idle.