I had the bad shifts from 3-4 and 4-5 and my tranny finally ate itself on a 1-2 shift in 4A when the truck slipped on the ice. Took a while to get it back, and when I did I still had the same odd shifts. The dealership left the Whipple program installed. It appears as if something wasn't installed correctly after the tranny rebuild, and the truck threw a wrench light after a week. The dealership installed a new valve body, reprogrammed the solenoids and it is now driving better than it ever has and the harsh 3-4 and 4-5 shifts are gone. I am still on the same Whipple tune. There is a TSB out for the harsh shifts on the 2018 Raptors that were built before May 15, 2018. Ford has acknowledged there is a problem and the fix is to reflash the PCM with their updated tune. This TSB came out in last September I believe, but Ford wouldn't allow my dealership to update the PCM due to the custom program on the truck.
It's interesting to me that the odd shifting went away after they replaced the valve body and reprogrammed the solenoids. I've only had the truck back for a couple of days, but it drives better than when I drove it off the lot new. Whipple has an update coming hopefully by the end of next week that they are saying helps correct some of the harsh shifting, so I'm optimistic for others that this helps resolve the shifting issues. My thinking now though is that the problem is in the valve body, possibly an air leak or something of that nature that causes this range of gears to have issues. I'm no mechanic by any means, so I may be way off base, but I'd be interested to know if your build date is before May 15th, 2018 since you are having these issues too. I'd get in touch with Whipple and have them put you on the list to send the updated tune when it is ready. You may see some gains with switching to MPT or Cobb, but I'm not 100% sure if their tunes help fix these odd shifting patterns either.
The only downside I have with the Whipple tune is the loss of the stock tune. I really think they need to allow people to maintain it in case the truck needs to be taken back to stock for troubleshooting items like this.
