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that's a fairly common problem on your mustang. There is a TSB for this issue calling for the replacement of the 2-3 accumulator piston. What happens is the fluid pressure leaks past the large diameter seal. There is an updated piston design to resolve that problem.
If you would like, I can email you the procedure to replace that piston.
I can also email you a copy of the TSB. but dont provide your email in this forum please
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I can't guarantee it, but it's very possible. The fact that there's a TSB on it indicates that it's a very common problem. When you installed the second transmission, it was acting differently at first. If this were a problem with something outside of the transmission it would have immediately acted the same as the transmission that was originally in the car. Considering that there is a technical service bulletin for this exact problem, it makes the most sense to perform the repair indicated in the TSB. The shift solenoids are located inside the transmission also so when you replaced the transmission, you also replaced the solenoids. If it were here, I would perform the tsb, unless it's already been performed on that transmission.
The TSB also applies to remanufactured transmissions since many of the remans have the OE accumulator
A TSB is a technical service bulletin. When a certain vehicle, or particular engine or transmission, etc. has an excessive number of the same issue, a TSB is issued to help us quickly identify the problem and resolve it better. Do you hear any noise coming from the torque converter area? A bad torque converter can rob the transmission of the required pressure and cause slipping, difficulty shifting between gears, lagging ( which it does sound like you have experienced?)
Here is a little self test to help diagnose the torque converter.
Did your transmission fluid in the last transmission look pretty bad?
maybe you do have a bad torque converter then. Do you hear any noise coming from the torque converter when you do the above test? If you hear noise coming from that area then definitely address that.
I can not tell you for sure what is wrong, and if it were at my shop I would not be able to say for sure what is wrong just based on what I know as of this moment. You have noted that it shifts from first to second, and it does not shift from second to third. This is consistent with a known problem on that transmission. I would perform the TSB and get a transmission flush. If you had nasty fluid in the last transmission, then most of that fluid is in your new transmission since almost all the fluid is retained in the torque converter and you are using the same torque converter. That's honestly where I would start.
I would think if the problem were with your torque converter then the symptoms would be the same with this transmission as with the last one. You should use the same flex plate from your original transmission.
You are in fact having different symptoms with this transmission as with the last one, correct?
And what is it doing now? it's starting off in over drive?
i'm going to hand this one off to another tech. I don't know where to go from here.