The trans ECM probably doesnt get a pressure reading back to it, it will just PWM the current to correlate to the appropriate pressure and assumes it is working, most trans don't have a pressure sensor(although that could be changing in very modern stuff, I'm not sure). Some of the new stuff can measure shift speed and adjust, I think thats why they added the input speed sensor to the 4L65E, which previously the 4L80E had it and the 4L60E didn't, but it still doesn't have pressure feedback that I am aware of.
When you get this one hooked back up, hook up a trans pressure gauge to the test port. I've ran the hose up through the shifter hole before, just remove the boot. Should be a 300 - 400 psi gauge, as the pressures can range from 100 to up over 300 psi depending on gear, throttle position, engine load, speed, etc. And check your pressures during shifts and stuff, and if it feels soft even if the pressures are good, fix it right away so you don't burn another one up. You should have it shifting nice and firm, not harsh, but it should be firm to last a while with any significant power levels.
I guess my point is, with all your troubles I would definitely hook up a pressure gauge so you know what is going on, and don't drive it until the pressures are correct and the shifts feel correct. For ~$30 you can pick up an ATSG manual for your trans and it will give you all the correct pressures and test procedures and also have a troubleshooting section that can tell you what to check.