It's probably not the tranny, what I learned
 

For longer than I hate to admit, I thought my transmission was getting ready to die. If I was cruising along in OD and the truck would start going up a hill and needed to downshift it would buck around like crazy. I'd push the OD button to turn it off, it would downshift and be ok. Then it would happen in 3rd gear, I was 100% sure it was the tranny. I'd gotten myself an ODB scan tool, a Veepeak Mini. When the issues first started, it didn't show any codes. 2 weeks ago I went to pass someone and it really started to shudder and the check engine light came on, but then went off. Plugged the scanner in and it finally showed a code, Cylinder 3 misfire.

I'd logged back in here and started searching to see if anyone had similar issues, and found multiple threads that had similar issues and coils/plugs being the culprit. I just turned over the 100k mark(I bike commute to work so truck doesn't get a lot of miles these days) and decided it was time to replace the plugs. I also needed to get new shocks so I decided I wasn't going to mess around with the plugs and let my local shop do it. They had done them before and knew the routine. They broke 5 of the 8 and that's after an overnight of soaking. They said their scanner showed multiple misfires, so I think I'm in need of a better ODBII scanner. Had 4 coils replaced as well.

Thing runs like new now. I put quite a few miles on it the past couple of days. Downshifts from OD smoothly now. I should have checked the forum when I first started having issues, but stupidly assumed it had to be the tranny.

Anyone have a good ODBii scanner they'd recommend?

Excellent.

I recommend one of those bluetooth OBDII scanners that you can hook up to a laptop and/or a smartphone.

I'd like to find a new OBD that is known to show all the codes. Mine never read any codes until recently, then it showed cylinder 3 misfire. The shudder had been happening for months, and I'd plug my scanner in and it wouldn't show anything. The shop said theirs showed a few other cylinder misfires. So it makes me think mines not doing a very good job.

That is why I am recommending a bluetooth OBDII scanner plug. This way it is software driven. You get a nice piece of software, you can read codes just like a dealer. Not to mention do cool stuff like play with Forscan.

I've got one that is just a plug and you access it via a phone app. It may actually work correctly, when the shuddering was happening, the check engine light never came on. Just seemed off that the shops reader showed more codes than what mine did after the check engine light finally came on.

The shop's reader probably was also showing pending codes.

You need to read the OBDII Mode $06 data and that data has a misfire count for each individual cylinder. This is totally different than a check engine light. This is the data that is stored while driving for diagnostic purposes. Torque Pro (available for android) will read this data and I used to use it while driving to determine which cylinder was misfiring on my 5.4L. There are many "code readers" that can read this data as well.
If you have more that 60,000 miles on the plugs, I would change the plugs and replace with OEM plugs and I would also replace the coil boots themselves. You can find the coil boots on rockauto sold in 8 packs. If you have a bad coil, replace with genuine OEM motorcraft coils that you can find on amazon for ~$45 each. Do not be temped to buy the cheap coils on ebay/amazon and stay away from "performance" coils like the accel coils - they are all junk and will fail in short order and you will be chasing and replacing misfires over the next year. I know because I paid the stupid tax to learn this lesson.

Denso coils are OEM and cheaper than Motorcraft. People also have had good results with Delphi coils.

Yup, any time you get bucking and shuddering under acceleration around 40-50MPH, that's your spark plugs needing changed. My truck did the same (plus on hot days, it sometimes took two times to start it.), I did a search on YouTube, and the consensus was to change spark plugs. Once, I did that, my truck ran so much better. BTW, doing it myself, following how FordTechMakuloco did it, I didn't break a single one (changing plugs requires heat soaking the engine)

BTW, I bought MSD ignition coils for my truck. They have 10,000 miles on them so far. (I did keep the original just in case)

Ah, poking around in the app now and I see the $06 Mode. Thanks for that bit of info!
Truck is running fine now, it's got new Motorcraft coils and plugs. Thing runs like new.