serious 4R100 trans problems!!!!!!!!

[o1whitelighting]

i have a 2001 F-350 4x4. bought used in febuary of 2007 with 94,000 miles on it. i put a ts performance chip in it right off the bat. man that thing would run, but the trans did shift right. i call ts and they told me that it was a programing problem. i sent it in and had it reprogramed put it back in and the same thing. so i said screw it and with a dp tuner. still did it but not has bad. i drove it for a long time put 107,000 miles on it and put a tranny in it. the funny part is that it already had a reman in before i got it (not cool). my dad and i pulled the tranny out and pulled apart and the clutches were smoked. rebuilt it and put in and nothing but problems. it was flashing the od light put it on the scanner and it was second, thrid shift default and third, fourth shift default. it would start out shifting fine and it went down hill real quick. messed with it and messed with checked the main plug going into the side of the trans noithing. couldn't figure it out. didn't touch anything it might sound dumb but it fixed itself. it didn't shift as firm as it should have i put a heavy duty clutch kit and a tci auto shift kit in it, and on top of that i have a banks trans command and the dp tuner and a shift mod on it. i put 5,000 to 6,000 miles on it and the trans started slipping. came to a stop light and took off and it slipped hard going into second. fluid was good and red and didn't smell burnt and the level was good. i drove it home and it got worse and wosre. it got so bad it was shifted into second gear and then shifted right back to first and it would jump between the two gears. it would finally grab second and then it didn't want to grab third. it would fight to do it. it was taking off in first second gear. and it got so bad first gear was binding up so hard you had to firewall it to get to move. i shut it down over night and drove it he next day and it shifted like a brand new truck, until it got warmed up to normal temp and it was back to the same old thing. it still sits today because i don't know what to do i need some seriuos help.