I am quite impressed with the TW chip in my brother's truck. The transmission tuning is good considering how the 4R100 works. It's partly mechanical and partly electric, so you can't do the nifty magic that you can with the all electric 5R110.
What I would recommend (I know this sounds hard) is removing the superchip all together and running stock. It will save your transmission. Your new transmission will not last running with a superchip. I would personally only run a chip from TW, DP, or Power Hungry Performance (PHP). They all have a good reputation for transmission tuning. I have only used the TW on my brother's truck, but I have been impressed with it.
The other thing is that if you tow (and want more power too) you might think about upgrading your valve body in your transmission. It would be a lot more effective than any software tuning on the transmission. It's easy to do with the pan off. It bolts right on underneath the transmission. It increases the flow to the clutches, and makes them hold better.
One last suggestion is that if your transmission goes out prematurely again, get a Suncoast transmission and torque converter. They're just about bulletproof, and they will handle any amount of horse power you throw at it. Although, it will still not last long with the poor transmission tuning that Superchips is famous for. The fully upgraded transmission in my brother's truck cost $3800, and the torque converter cost $1200. The transmission has incredible firm shifts. The torque converter is out of this world. It has a higher stall speed, so you can start loads way more easily, and it won't burn your fluid as easily. It also has a triple disk lockup clutch. At idle speed you have to hold your foot on the brake, or your truck will drive away, even up hill or pulling a trailer. That's all the torque converter.
BTW, if your wondering why my brother's truck needed a new transmission if the tuning was so great from TW. Well there are two reasons.
#1 is that that truck towed every oversize, over weight, illegal (size and weight) load we threw at it with no chip or tuner at all. It got horribly abused. This lasted from when he got it (40K miles) till the power train warranty ran out (100,000 miles).
#2 at 100,000 miles he installed a superchip. He ran it on the high setting all the time, and he's not exactly gentle with his truck (see #1). He also didn't have a transmission gauge while he was doing any of this (only the useless dashboard gauge). The transmission went from normal operation to not working so great in about 15,000 miles.
He installed the TW about that time, and the transmission got better immediately, but I think there was already damage done, and it was just by the grace of the TW chip that it lasted another 15,000 miles. He figured that he might as well get a good transmission when he replaced it. We did the labor ourselves, so the overall cost wasn't much more than a shop putting in a re-built. And I know it was done right.
Actually when his transmission went out, it may not actually have been the transmission that failed. The torque converter exploded, so it definitely wasn't moving, but the transmission may have been fine. Although with that much metal garbage floating around the transmission afterwards, I wouldn't think the transmission would be much good for very long.