Have you tried the truck on stock tuning to see if these issues go away? I know when it's cold and I have a hot tune installed on my truck, it is like driving a light bulb, on or off. Very similar to driving a two stroke actually.

mine runs the same with or without the tuner its just in the morning before the tranny warms up then it is fine so i dont know whats wrong with it

If there is actually a problem, I highly doubt it's actually the trans itself. Probably some sort of injection issue and the trans is just trying to save itself from funny shifts.

Does the trans shudder at all when going into reverse? Any delay when shifting gears?

I know you said you "fixed" your FICM, but did you ever actually test the voltages on it? How are the batteries? Sorry, this thread is old and long and I haven't brushed up on it lately... just thinking out loud here.

the batteries tested at 12.4 and the ficm tests at 48v steady with key on and running there is no shudder in the tranny it shifts fine if you let it warm up after you drive it once it is fine the rest of the day no matter how long it sets that day

12.4 off the truck right? Hopefully not 12.4 on the truck...

It'd be nice to have a scanner on it to see what is going on... I'm leaning towards it NOT being a trans issue at all.

When is the last time the trans has had a fluid change though out of curiosity?

i hooked it up to a scanner it didnt show that anything was wrong the batteries read 12.4 installed in the truck with it off

You need to remove the batteries and have them load tested. You could have a dead one sitting there and the good one is throwing off your readings. If one is bad, it's just going to kill the other one quicker and possibly take the FICM out too.

Thats what mine was doing with the shifting part! minus the cranking problem but the shifting is just the same. put a ficm on from mike and it runs like a beast now! also cleaned turbo but that was a diff issue

It cleared up your shifting issues too? I figured it would, glad it did!