Well that sucks.
I am actually seeing three piston variants on RockAuto - 90-94 small dish, 95-00 big dish, and 98-00 slight recess, almost a flat top.
I'm not really sure what to suggest. You could find a different machine shop and have them go through your heads again and hope they use better valve seats (I still think they used cheap parts thus the failure) but that is a tough call, nobody here will know what brand of seats are good and which ones are not, I kind of doubt that most machine shops would know either.
You could put older big chamber heads on it but you lose compression ratio that way with your pistons. Not great
You could use older (90TM or 93TM) heads and older small dish pistons in it, basically back to stock - wondering if this might be the way to go with your ECM, you will have money into heads no matter what route you go
If you fixed what you have now, you could try running a later 93 or 94 ECM or do an OBD2 conversion on it and run '95+ stuff. Late OBD-1 ECM seems like somewhat of a gamble. OBD-2 conversion brings a lot of other things into the mix (cam sensor, EGR, etc.)
But maybe this just happened with shit valve seats and good ones will get you up & running indefinitely.