O2 sensors with 94000 miles on them should be changed. Period. Your car will run its best when the feedback the computer gets is most accurate. They could have been damaged when you did the exhaust or when you did the heads. Who knows. Just consider it money well spent no matter what the outcome.
You should probably hook up a fuel pressure gauge to make sure that your FPR hasn't gone south on you. Make sure you have 37-40 psi and that it goes down if you apply vacuum to the vacuum port. You may also want to perform a leak down test.
You should never need a custom tuned chip to run normally (maybe to smooth out an idle with a radical cam or something). They come in handy when you want to run leaner or richer than stock, or with a different timing advance curve.
Did the mechanics get the codes from the computer or did they just put a dab of oil on their finger and taste for problems?
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351W 89 Mustang GT Convertible