TCM will not Communicate?

So, I have the truck listed above with an extended cab about a week and half ago on my way home from work I made a stop at the store. No more than 10 minutes later. When I started my vehicle back up the ABS and check engine light came on. The Speedometer completely stopped working and the truck wasn’t accelerating normal when I pressed on the gas pedal and I started hearing this clicking sound coming from my dashboard every time I hit the brake pedal, and it also wouldn’t show me what gear I was in. This morning when I started up my truck to go to work there was a lot of smoke coming out from the exhaust. But after being on the road for a bit it stopped throwing smoke from the exhaust although the same problems were still present prior to today. So, I stopped at autosome so they could give me codes for the problem. I forgot the code that came up but it was a a code for a no communication with the TCM and another code for the rear wheel speed sensor So I got on the internet and did quite a few researches to try and figure out the problem. After an hour or more of research, I ended up buying a speed sensor and rear wheel speed sensor. I installed the new speed sensor hoping it would fix the problem, but it didn’t. So, I continued with the next step to try and install the rear wheel speed sensor but when I pulled it out of the box. I noticed they’ve had given me a used one. Plus, I had a really hard time trying to locate it on the truck to get it installed. I wasn’t able to find it. So, I thought maybe they gave me the wrong part. I went back to exchange it for a new one and to tell them they might have gave me the wrong part. But they reassured me that my truck does have the rear wheel speed sensor. So, one of the employees came out to try and help me locate it. But failed as well. So where chopping it up a bit trying to figure out what the problem could be after a few minutes he ended up offering to run a code test with his personal obd2. And on his the only code that came up was the U0101 saying something about not being able to receive communication with the transmission control module so he told me he was sure that was the problem so we went back into the store so I can buy a transmission control module but they didn’t have it in stock so they ended up ordering one so I can pick up tomorrow in the afternoon.
Oh yes, I forgot to mention that right before I stopped at the store prior to the problems starting. I got on this road that had a lot of potholes and was badly maintained. That I even said to myself “why did I come through here” but never thought nothing of it. Not sure if that has anything to do with it but just wanted to throw that in there.
I ended up getting the TMC so me and my buddy installed the new one and lights came off the dashboard showed me what shifting I was in and Speedometer started working but we knew it needed to get reprogrammed, so we took that one off and put the old one back in.
So fast forwarding to yesterday I finally found a place where they were able to reprogram the TMC for a fair price. But unfortunately, they couldn’t program it because they said it didn’t want to communicate with the main computer. I’m stuck and don’t know what to do now.