Do you have a scanner that you can see which cylinders are misfiring?

I'd also check the PCM connection. Disconnect it, check the contacts, use some electrical cleaner, and reconnect.

With the engine running spray some carb cleaner around the throttle body, valve covers, etc to see if there's a vacuum leak. You'll know if there is one because the engine will rev up when it sucks in the carb cleaner.