Are they running a chip?
As long as the hpop has the right angle or a greater angle than factory it should be fine. The early 99's had a 15 degree pump and the late 99's switched to a 17 degree pump.
If I recall correctly after 97 all the ipr valves are the same. (I know someone will correct me if I'm wrong)
The injectors in the early 99 are supposed to be split shots according to the 98-99 coffee table book. If the chamber size is different as long as the nozzles are the same as the original injectors it will never know the difference.
The idm will be compatible other than maybe a lower voltage output than what the "blue motor" was designed to run with, but it will run normal. (I've used an idm out of a 97 in an 02 in a pinch and I could not tell the difference and there was no light)
I guess if it were in my bay I wouldn't get too worked up over the transplant and I would diagnose it like it was normal. But when it comes down to replacing injectors I would push like hell for a full set so that they all match.