1999 Camry misfires at 4200 rpm

What would cause a 1999 Camry to misfire/act up at 4200 rpm and above?

We very recently had the engine replaced on our 1999 Camry (V4; it had 110,000 miles on it) while on a trip. There were some issues with the repair that have been resolved, but our local mechanic is having a very hard time solving one last problem they found. The car has been in the shop locally since last Monday (7/18/11).

The mechanics that installed the used engine do not know the exact year of the engine, but it is matched based on the vehicle VIN when the part is sourced. The manager said it was probably the 2.2L engine and within a year or two of 1999. The engine meets federal emissions standards, not California’s (as would be expected). They used the existing wiring harness from our car, as it is part of the engine block. The only new parts listed were the water pump, plugs, wires and timing belt. So my guess would be that the other items were transferred from our old engine.

Otherwise the vehicle drives fine (according to our local mechanic).
It is not the crankshaft sensor as it produced the expected square wave. They were initially pretty confident on this being the source of the problem on last Tuesday evening.

It is not the timing belt. It checked out fine.

They do not think it is a sensor issue since there are no electronic codes coming back so that is why they think it is a timing issue.

A few things they are considering:
1. Non-iridium sparkplugs were installed in the tune-up of the engine.
2. The fuel pump/pressure gauge.

In talking to the mechanic on Friday, he mentioned that the MAP sensor was reading 5-6 Volts? mV? (whatever the units are, but he said it was voltage) high. The upshot being that the vacuum in the engine at this level rpm (4200) is too high.

One of the problems is testing it at this rpm level since it is that accelerating up to highway speeds is the only thing that seems to cause it. I myself did not notice it while driving it home. Another compication is that there are no error codes.

I just want to know what should be looked at and have this issue resolved.