Probably tires, but not flat spot. Flat spots go away once tires warm up. Either balance weight (hopefully) or see above....
Misfire might be another iffy connector.
Clunk: driveshaft splines loose (did you relube shaft?), loose bolts, or u-joint bad.
As for perky, the engine has more friction now (breakin) so you lose some there; and the ECU is still learning the new setup.....
The vibration... Well, before I parked the truck in 2013, the tires were fresh and balanced well. I cleaned and relubed the U-joints and spline and was careful with re-installing them, so I'd be surprised if they are loose. The amount of vibration feels like tires, but could be in drive line. I will check it out, and then have Discount Tire look at the tires... geezzz I would hate to have to buy brand new tires again!... but I should have blocked up the truck.
The clank at start and back up... that sounds like very sharp metallic clank with a very slight lag. I will check motor mounts and drive line. I may have to put it up on jack stands and get under the truck with my wife doing the shifting test?
The misfire... it has a very slight misfire during low RPM between off idle and 25 MPH, just driving slowly in 1st gear. I don't think its spark or ignition timing. It could be air/fuel mixture? I will pull the plugs this afternoon. I will do some diags on the ignitor and coil. Yes, the issue could be 3 other bad injector connectors!.. or some wires in the harness that are not getting a solid connection or ground.
I am still wondering about this cam profile. IF, after about 200 miles, and all my normal "tweaking" and verifying all systems are performing normal, it doesn't smooth out, I may consider swapping in a different camshaft. I can re-install the stock cam that was in the old head as a test.
I don't have the pleasure of previously breaking in a rebuilt 22RE so I don't have anything to compare to. I realize at only 45 or so miles on a break in its still "stiff". I have read that the ECU "learns", but I would like to understand what EXACTLY does that mean. The ECU and input from the sensors have electrical ranges and limitations - what are those limitations?
This rebuild has been a real challenge and interesting. I sincerely appreciate all the input, great advice, shared knowledge, and the poking fun at me. My truck is my second "hobby" right now, and it would not be as fun if it weren't for all of you who contribute to my experience!! Thank you with HUGE-ness!