Shaking 3.0 and wonky idle

Need help here because I'm stumped. Short version- My original '92 3.0 overheated at 260k miles. Instead of fixing, I got a salvage yard 01 from a taurus and converted it over. After 4k trouble free miles, something came loose inside it and I ended up pulling it. Replaced it with a 07 Taurus pull with 120k. Swapped in new oil pulp, my pan, ranger head gaskets, my '92 balancer+flywheel (worked fine with the 2001), my intakes, tin, fuel system, accessories, etc, just like I did on the 2001. Also did new cap, rotor, and wires along the way.

Fast forward to now and after 5 months with the new engine (maybe driven 400 miles), The engine seems to run fine and idle ok, except for sometimes idling to 2k, but it also seems to have a shake and a "roughness" when accelerating. Seems to not be noticable above 2k RPM. I discovered that I had swapped the wires for #4 and #5 at some point, and fixing that helped, but it didn't really fix the original problem.

In reading, it seemed like maybe the dreaded recessed valve, even though it's an 07 engine. I just finished doing a compression check on all 6 holes are between 132-140 dry, #4 is the 132, #2 is 136, the rest are right on 139-140. I didn't do a wet check yet, but that puts all holes within well within the 10% rule.

I did an OHM check on injectors 1-3 and all are between 14-17. I'll be checking 4-6 in the next few days.

The wires were change during troubleshooting, so I think they are ok. Could this be a bad plug, rotor, cap, injector, something else? Rotor, cap, and plugs have 4k miles on them. What the heck am I not thinking of? I also have to sort the occasional high idle. I just replaced the IAC and that helped some. I can't find any vacuum leaks.

If anyone has any ideas, i'd appreciate it before I pul what's left of my hair out.

Have you ever replaced or inspected the camshaft synchro and sensor?

This was the cause of my own mystery shake in my 99 2wd

Also since the plugs are new-ish, did this shake start showing up around the time you replaced the plugs? I've heard mixed reviews on using any plug other than motorcraft as a lot of our 3.0s don't seem to play well with anything else.

Good thoughts. The cam position sensor is a no-go, my truck is the older distributor setup, so no sensor needed, but I will say, it feels like a cylinder out of time.

I haven't ruled out a bad plug. I'm using a new set of the same Autolite 764 coppers I've always used in this truck. I would agree, even these older trucks tend to prefer Motorcraft/Autolites. With my dizzy set-up, I've always found the coppers to be better performers than platinums.