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Did everything get plugged back in? All the wires to the 4WD shift motor? park/neutral sense switch on the transmission? vehicle speed sensor on the transfer case?
Im having the same problem...but I haven't replaced my auto tranny, I might need to but I haven't done it...I have to let go of the gas in order for it to go into 2nd gear.
Sounds like the shift motor is dirty. Probably just coincidence that it stopped working just after putting the transmission back in. You can pull the shift motor and clean it, and it will usually work just fine. See www.glue.umd.edu/~singletn/exp.html
I would just try disconnecting and reconnecting the shift motor. Sometimes it is difficult to tell if it is fully connected. I actually took a pair of chanel locks and gently squeezed the connector together. I repeat....gently. The connector only moved about an eigth of an inch, but that was enough to make the connection. Now, no flashing lights.
I have a 92 explorer same problem at the beggining of last winter i cleaned it and it worked great, few uses later stopped worked again the brush's and the brush surface were dirty again, so i cleaned it again, i sanded the brushs with emery cloth and also the brush riding surface with emery cloth i also use a Q-tip and CRT cleaner to make sure it was all clean, assembled it worked great few uses later same thing cleaned it one more time and at the end of last winter it stopped working again, what is the problem with this thing do i need a new shift motor or what, or am i missing something here?