5R55E problems

[FLYIN 5.0]

Ok experts I have a problem that makes no sense to me and could use all the help I can get.
So I have a 99 4.0 w/5R55E trans Check engine light is on though the codes are never for the trans. I have had the codes read by my local shop and they were stumped because when they checked each engine sensor or component they checked out OK.
Everytime I reset the CEL the trans slips going into second gear. It will do this for a few stops and then clear up and the CEL will come back when it slips.
The trans will also slip when I refuel the truck. Only a few times but it happens at every fuel stop. Again after a few times it clears up and no longer slips.
At all other times the truck drives great with no other symptoms at all other then the CEL being on.
I have had the truck into the ford dealer and had the PCM reprogrammed with all updates. The CEL was back on after ten miles down the road.
Any ideas at all would help as I am stumped. My next step is to drop it off at the dealer and have them run up a huge bill trying to figure this thing out. Thanks

 

[chopperb]

What is the codes that are coming up?

 

[FLYIN 5.0]

Bank 1 lean, Bank 2 lean and something about the evap system. I also had the trans serviced and the guy said it looked nice and clean and he thought it might be a spec of crud caught in a solenoid. He said he could rebuild the valve body for $750 and of course I passed as I know I can order one for $250 rebuilt. Im stumped. None of it makes any sense to me.

 

[PopRichie77]

When bank 1 and 2 are lean, almost always it means the intake gaskets are leaking and should be replaced, replace both , top and bottom. Need to know more than something about the evap system, need actual code. Engine problems must be fixed first before trans problems as the computer uses engine sensors to properly shift the trans.

 

[FLYIN 5.0]

I will find out more today. I just had the intake gaskets done a few weeks ago.

 

[FLYIN 5.0]

Ok I might be on to something. I just bought this truck a few weeks ago. I picked it up cheap and have been going through it fixing all the PO screw ups. Well he had installed a K&N air filter. I think all of you know if they are over oiled that it will foul the MAF. So I cleaned everything and reset the CEL. Took it out for a long long drive and put it through the paces. Ran good with NO slipping and no CEL. I wont pat myself on the back to soon though as I will give it plenty of time before I will say "it's fixed"