1990 could have a 2.9L for 2 reasons, 1) it was an early 1990, marketed as a 1990 but it was actual an 89, 2) there have been situations that things exist that aren't supposed to, i had an 88 bII with a 2.3L v6, yes, a 2.3L v6, that motor isn't supposed to exist in north america period, but yet, i had one with that motor, looked just like the 2.9L but shorter by atleast 6"... sat really low in the engine compartment...
the knock sensor, if present, and if the computer is looking for it, but not getting a signal from could cause your problem, if the computer is interpreting the "signal" or lack there of, as a ping, it could continuously retard the timing to the point that the motor barely runs, or stalls out completely... your spark would be just way too retarded...
drilling holes in your exhaust before the o2 will never help your situation, why, might i ask, did you drill them? i would plug them, reset all codes (which you should pull anyways) and see how it runs