Cool, at least you are getting a code. I was having some jerking/misfiring like for the last 5 months. I changed all injectors/coil packs, charcoal canister and valves, MAF, sparks, a few vacuum hoses, fuel pump and fuel filter, PCV, timing belt, Cat Converters, transmission fluid exchange (not flush), o2 sensors. Yes a bunch of stuff that was way over due anyways, I got 284K on my 2003 Sequoia. No mechanic could find what the issue was, the last shop where I took it had it for two days and since it wasn't showing any codes, except for "something to do with the ECU" and the tech who drove it said I seemed to be something with the tranny, like a torque converter, which I was also leaning towards, they didn't charge me anything which made me smile
..I went back the next day and brought them a box of donuts ($3.99) I put in 2 tubes of shudder fix and it seemed to run smoother, but the shudder/hesitation/misfiring sensation was back again. Anyways, the reason I asked about any recent electrical changes was because in my case, I discovered what the issue was....ready? My turn signals!!!! I had discovered that the turn signals were disarming the cruise control and after reading about this happening to others, someone mentioned that that had to do with the wiring to the tow kit harness and I let it go as the cruise control wasn't a big deal to me. However, I didn't think about the turn signal having to do anything with the hesitation issue until last Saturday while on the highway I realized it. Since I'm one of the few in a million turn signal users, I unconsciously use it without even noticing and then I told myself, wait a second, this is crazy! Yes, it was caused by me changing all the tail light bulbs (turn signal, brakes, reverse) to led. For I read somewhere, the led circuitry or filaments had something to do with sending a signal to the brake lights or the actual ECU thinking you were applying the brakes while on the gas pedal. So, I swapped all tail light bulbs back to normal and the hyper-flashing device back to the original and NO MORE HESITATION until I read more of what device(transformer, diode, etc.) I need to use if I decide to go led again. I kept the reverse light as led as it wasn't part of the issue. I apologize for the long story, but I'm sure many out there are probably scratching their heads too and losing sleep trying to figure out what's going on and perhaps they have the same issue as me and hopefully I might be of some help
..In your case, it looks like something different. Good luck and I hope you get your truck fixed soon. Keep us posted.