Just a tip - lots of stuff like this has been extensively covered here on Explorerforum in the past. Just use the search featrure built into the header bar of the forum and you'll likely get more posts to look through than I could describe.
Now back to your problem...
I would say that the two issues (off-roading and installing the auto start) are unrelated to a blinking OD light.
The blinking light is a warning from the transmission computer to let you know that something is going haywire with the transmission electronic controls and/or speed sensors. That could be almost anything from a leaky/loose valve body (bolts generally need to be retorqued to factory specs and/or blown valve body plate gasket) to solenoids not working correctly (plugged, pushed backwards out of their bores, and failed are all common) or some other issue that could cause a speed sensor to mis-read such as a frozen sun gear cluster on the forward sprag.
Starting with the simple stuff and working towards the difficult (the best advice for trouble shooting), I would start by getting the codes read for the tranny. That will give some indicationas to what is happening inside the tranny computer. Next, I would proceed with dropping the tranny pan and doing a general inspection to make sure that none of the solenoids have backed out of their bores (Ford used some brakets that allow this to happen once in a while) or a blown valve body gasket/low torque on the valve body. If this fails to cure the situation, you will likely have to tear into the tranny itself, either to clean or replace the solenoids, or to inspect the sprags.
We played around in 4 wheel drive a lot over the past few snowy weeks, and also just had a remote started installed...could either of these things have contributed to the problem?
