TROUBLESHOOTING HELP DESPERATELY NEEDED PLEASE! SORRY FOR THE LONG POST!
BACKGROUND:
I have a 2002 Toyota Camry LE with the 2AZFE engine and A/T with 245,000 miles on it. It had the dreaded stripped head bolt holes in the block problem which was recently "fixed" by me with Norm's inserts

. I don't recall the car having the following problem before the "repair" was done. i.e. - please help me figure out what I screwed up

.
THE PROBLEM:
The car starts fine, but has a very rough idle - sort of a knocking/loping sound. The car, however, doesn't seem to idle near as rough when it is warm (i.e. at stop lights or in parking lots). The car usually gets up to speed fine, but most notably, when cruising at low load speeds (like in overdrive at 55MPH on a relatively flat road) the car begins to shutter and shake and loses some power. When this happens the car will downshift in order to compensate for the slowing speed, causing the RPMs to naturally go up and the smooth engine performance to return until it upshifts again for cruising, thereby causing the RPMs to drop and the stuttering and shaking to return (not cool unless I brought my Margarita mix with me). This problem usually seems to happen below 2,500 RPMs. If I am cruising at 70MPH on interstate it is relatively smooth as it stays slightly above 2,500 RPMs. Lastly, the car, on occassion and when starting off cold for the first trip of the day, will have trouble getting up RPMs and getting up to speed with very notably reduced power. The car's Check Engine Light is on and is showing misfires in multiple cylinders. The light sometimes flashes especially when the first misfire of a trip occurs or if it is a severe misfire.
WHAT HAS BEEN CHANGED/CHECKED:
When I installed the inserts I also replaced the head with a rebuilt head which had different, new, or rebuilt camshafts, valves, valve seats, valve springs, and lifters. I also installed new head bolts and washers, head gasket, valve cover gasket, intake manifold gasket, exhaust manifold gasket, water pump, and spark plugs (denso iridium). My mechanic has checked the following: switched around coils and plugs to see if the misfire codes followed the coils or plugs - they did not - the misfires remained in the same locations. He also did a BG-brand fuel system cleaning service. He checked the compression - all cylinders tested fine. He checked the timing - which was correct.
The car does have some miles on it and it did sit around for a while before it was repaired, but I don't remember the car having the problem before the block repair. I am far from being an experienced mechanic so who knows what I screwed up!
My mechanic and I are at a loss.

Does anyone have any suggestions as to what else this could be? My guesses are too numerous to be able to afford to change out each part: EGR valve, MAF sensor, O2 sensors, IAC valve, fuel injectors, ECM, or something not being right in the "rebuilt" head. Any help would be greatly appreciated!