dont know what to do!!

Ive got a 99 3.8 windstar, just had the engine replaced w/ a used one. I had tranny codes coming up before the motor swap, now ive added a 1309 code. the shop that did the work thinks the tranny problem is related to the 1309(misfire code) they usually happen at the same time.any thoughts?,
another observation is that i had ford flash the computer, they told me that i had the most recent programming and they cleared the eeprom, while driving the 20 miles home the tranny shifted better then new until it relearned its settings, then it clunked, the od light flashed and it shifted roughly after that. once I get past 3rd gear the od light goes off and everything seems fine, but if im driving in stop and go traffic the od light comes on occaisionally. Ive had the filter and fluid changed and i replaced the output shaft speed sensor(the one behind the driver side wheel) Any other sensors i should be looking at. I really need to eliminate the tranny codes so I can isolate the 1309 code and see if it is possible that they are linked, oh the tranny code is output speed sensor circuit, any answers are greatly appreciated. Marc

Hello

What code (number) did you get from the trannie?

Regards

Dan

tranny code is 0720, output speed sensor circuit, I replaced the sensor already, the problem occurs after the van is warmed up and driving in stop and go traffic/slow speeds, it runs great cold. Thanks

Check the transmission range selector connector located at the top of the transmission. These are notorious for screwing things up with the transmission. First thing to check is for corrosion or poor fit. If that checks out, you'll have to use an ohm meter and check the readings at each selector position.