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I just installed a "bargain" (reads e-bay) '87 HyperTech Stage II chip but haven't had a chance to test results yet. However, instentaneous mileage seems as good if not better as with the stock chip. I think this is a good indicator of efficiency and hence emissions.
If you're concerned about emissions, try my spark plug "trick" (on my site) to increase burn efficiency, upgrade your ignition system and make sure your motor is up to operating temp before you go to the emissions check center.
I don't think the Stage II chip will of itself would cause you to fail emissions.
The Hypertech Stage II chip only changes engine operating peramiters (timing & injector duration) at WOT. It also turns the fans on earlier but this shoukd not effect emitions.