5R55E wouldn't shift today

[mixwhit]

got in the truck ('03 4.0L 2WD) about noon (first time in it for the day), started up, and it wouldn't shift. i moved the lever to R, heard a bit of a normalish noise, but it was like i was stuck in neutral.

tried it a few times, including D, maybe also 1, got out, looked to make sure nobody blocked my wheels, then got back in and it very clunkily shifted into R, made a big noise. same noise shifting into D.

drove a few miles, parked, came back ~1.2 hours later and this time it was clunky and jerky but worked first try. drove around for a while until engine temp gauge showed it was warmed up and then checked fluid level, found it looks overfilled (see photo).

while warm it seems fine. shifts smoothly.

I had a new engine put in it about 3 months ago and haven't looked at the tranny fluid since before then (I had them to a filter/fluid change w/ the engine install).

any ideas of what's going on? i wouldn't think an overfill would cause this. this may be the coldest day we've had in a while so maybe it's cold related?

oh, i should probably add that shifting seemed fine once it goto the correct gear

update: i should also add that i've been hearing a bit of a clunk lately. was presuming it was ball joints needing replacing, but havent' been sure as sometimes it sounds like it comes from a more central location (e.g. underneath me rather than at the front wheels). is there anything leftover from an engine swap that could have led to this? bell housing bolts loose or something?

http://imgur.com/6oeog

 

[Sasquatch_Ryda]

Engine idling in park while checking?

That fluid was just changed? It doesn't look very bright red like new fluid would look.

 

[mixwhit]

yes, idling in park while checked.

it was a pan drop and filter change, not a flush. doesn't that only swap about a 3rd of the total fluid or something?

 

[Transmarobirdeater]

I'm having issues with a noisy shift as well, also had an issue with being stuck in nuetral. I replaced seperator plate with gaskets. It didnt help at all. In fact my transmsion was out of an 04 explorer, It had the bonded gaskets on seperator plate it looked to be in good shape. No sign of blowout. Im guessing Intermediate band trouble or valvbody bores are full of trash. Dont know but im working on it. Im already hunting for a back up.