You should ensure all your ECU connectors are firmly seated. You might want to disconnect and reconnect all of them. Listen carefully for that "click' sound the lock makes when the connector is fully engaged. Don't forget to disconnect your battery prior to unplugging the ECU.
Don't worry about damaging anything. Fueling is primarily done off the upstream sensor so your engine won't be running too lean or too rich.
BTW, how's Stage 1 boosting up there in high altitude? What kind of octane are you able to run? Is your PT a manual or auto trans?
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