GRRRRRR. Shifting issues E4OD

Ok, so here is the story. Bought 97 F350 7.3 with a brand new Jasper E4od 1 year ago. Bigger injectors, TS chip, 6 inch lift etc etc. The thing is a beast. ABS light was on when I bought it. Had scanned but they couldn't come up with anything. Torque converter blew 3 months later. PO apparently took it on the sand a lot so no surprise there I guess. Not sure if the TS chip running in position 6 all the time had anything to do with it. Got new torque converter installed. All went well for a while.

First thing that started to happen was I was heading up the freeway pulling 3000lb boat and as I went up a hill I had this like micro sputter between 55 and 65mph. It was one of those things that I could hear more than feel. If I wasn't paying attention I wouldn't have known about it. So after reading and reading, I decided to replace the MLPS since it was the original on there. I also replaced VSS and did a rear end fluid change. ABS light went off for a couple minutes but then went right back on. I did notice a slight chip in one of the teeth of the tone ring but it wasn't huge.

So then a couple weeks later, I was pulling a very light trailer heading to the dump and as I approached a stop sign, the engine died and what was weird is it felt as if I were in a manual tranny and forgot to push in the clutch (like the TC was still locked.) Started right back up and on my way I went.

When I bought the truck, it had 33's on it but I put 35's on it (4:10's). I have the newest Edge monitor (can't think of the name right now but it's not the tuner) and anyways I have it set my current tires to read speed accurately. The speedo is about 9mph slow due to the bigger tires and the PSOM is locked out because of too many changes.

I've always thought I had a little erratic shifting so while reading about the little sputter, I realized my speedo could be affecting my shifts. So I bought a new PSOM and installed it and in the PSOM I installed LED backlights.

After installing the new PSOM, I re calibrated it to my tire size. However, it now drives like total crap. It won't shift into 3rd gear while under load. The fastest I can get is like 35mph. Whats weird is my Edge tells me what gear it is in and sometimes it seems like it is wrong. Going up a hill, my RPM's just climb but speed stays the same after about 39ish. Once the temp comes up a little bit, I had no reverse. I'd have to turn it off, let it sit a bit and then eventually reverse would work. When cold R works fine.

So I dropped the pan and pulled the VB. I bought a tugger kit and installed it. The magnet looked like a sea anemone! All the shiny grease like stuff but there was one tiny piece of flat metal about 4mm wide by about 10mm long and very thin. There was quite a bit of material on the bottom of the pan too. Replaced filter, couldn't drain TC because there wasn't a plug. Fluid wasn't "burnt" or black but just looked like dirty cherry. I refilled and now it gets to 3rd it seems but definitely won't go into 4th. On my way back down the hill, I pickup speed and get to 55mph and per my Edge monitor, it shifts into 4th gear, but when I step on the gas it feels like the TC is not locked and the RPM's start to go way up. Also, reverse works fine now when warm.

I tapped into the purple/yellow TC lockup wire and just took it out for a test drive and the TC is locking. While sitting in D, it instantly kills the engine so it doesn't appear to be shot.

I also read about the brake lights issue - top of cab was out as was one of the back ones. Replaced them all but no change.

I was hoping to take this truck on a 2 week trip really soon and cannot get it into a reputable shop before I was planning to leave. Any help diagnosing or advice would be extremely appreciated!!!

I would think if the 3rd clutch pack was gone, I wouldn't have reverse, right? It sounds to me more of an electrical/sensor issue vs mechanical in the tranny - even though I did have that once little piece in there on the magnet. One thing I forgot to mention, I did pull a very very heavy 5th wheel one time over the mountains that slightly overheated the engine - tranny was fine until I turned the engine off at the top to give it a break and then the OD light started blinking. That was back in October and after resetting it, it drove fine for many miles until these issues started coming up.