ls1mx5

Does anyone have trouble getting their car to perform a CKP system variation learn procedure? My car has been misfiring lately, and had a code for the crank sensor so i replaced it with a new chevy part, but the misfire is still there, with no misfire codes! I have tried using HP Tuners to perform the learn process for the new sensor, but it does not complete. The factory service manual mentions: if the pcm sees "no change in brake switch input, the learn procedure will not be allowed." My car is a conversion, and I did not connect my ecu to the cars brake switch. Am I missing something here? The engine and ecu are 98 camaro ls1 parts...

THANKS
Karl