for your info 4l60
I would bet that it had a handful of transmission related codes. The original PCM you bought was programmed for a 4L80E and not a 4L60E. The 60E and 80E shift solenoid "B" operate exactly inversely to each other. In other words, in a 60E when it is commanded on in an 80E it will be commanded off. This happens in each and every shift sequence. For the purpose of swapping an 80E into a 60E vehicle what we do is simply invert the commanded signal to solenoid B by using a simple Bosch style relay. In other words, when the PCM commands it to be on, in reality it is off and vice versa. The PCM doesn't care that we made the change because it sees the gear ratio and rpm changes it was looking for when it commanded a particular shift sequence, plus the electrical circuit is intact... so no codes are kicked. There are a few modifications that need to be made in the shift scheduling and converter lock up software side of things, but that's another topic for another discussion. The schedule for solenoid "A" is exactly the same. That's why we can use 60E software to control an 80E. The 60E software doesn't care if the 80E has an input speed sensor in most applications. However, the 80E software has significant issues when trying to control a 60E unless the 60E is a late unit with an input speed sensor... but who takes an 80E out and puts a 60E in it's place? I haven't ever explored that swap! LOL....
The 60E was never used in a 3/4 ton truck that I am aware of, therefore you were trying to command a 60E with 80E software. My point is, it's a little more complicated than just an input speed sensor.
In your comments you mentioned that "all the experts said it was smoked"... I'm curious to know if all the experts had the same information you did regarding the combination you put together. In other words, did you post a thread about it somewhere, or did you try to apply your symptoms and conditions to someone elses symptoms and conditions? I'm not ******* you, just trying to make the point that we as experts are only as good as the information we are given. And I know the other experts around here well enough to know that they are some pretty bright fellas, there is no doubt they are the cream of the crop, the best of the best at what they do in many cases. The shops that are represented here, and the Pro's that work in them push the envelope, most of us have done the conversions years ago that folks like yourself are just now doing. Some of us pioneered the swaps that are very popular today in fact. Many, many many countless guys have saved untold amounts of money in repairs over the years by coming here and asking questions and getting solid advice from industry leading professionals. Those experts do it for no compensation 9 times out of ten. And those same experts will continue to do so for years to come too!

I would like to read the comments in the threads that you referenced as sources to help with your problem. The reason is, I've seen guys fall into the trap where they do not ask questions, provide insufficient information or they just do not speak up and research the problem they are having and go about the diagnosis with less than solid and complete information.
I'm glad you solved your problem! There's nothing like beating your head on the wall for days or weeks only to find the solution. I've done it countless times and I know all the Pro's here do it too. Good job buddy.
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