98 Ram Sticks in 2nd gear after warming up

Here the thing, I just had a rebuilt trany installed w/ the large aftermarket cooler a year ago feb, After the trany warms up about 4-5 miles it wants to stick in 2nd gear, I can shift to nutural and back to drive and it will shift. It only has 10,000 on the rebuild, I checked fluid level is good I added a court of Lucas Trany fix. No help! I checked my trany fluid by pumping some out of the cooler installed in front of radiator and it is a dark non-transparent dark grape looking fluid but pumped a 1/2 court in 2 seconds that tells me nothing is pluged. I also changed the speed control sensor and did notice some fine metal like matallic paint nothing real big, I would guess this is some what normal. Also notice once in a while a little clicking noise from the what sounds like it is coming from trany but not sure, Anybody have any similar problems or know whats going on with this or have any good suggestions to try and save this trany? I'm going to do a filter change and also think about a fluid change. Can I pump the fluid out of the trany long enough to replace it or should I try to pump in the same amount I pump out? Oh Ya This trany always from day 1 have a whining noise in low gears.

Thanks
Tom