Hi Daniel,
It may be a few things. The engine could be slightly out of time so one or more of the cylinders are firing out of time causing a knocking or thumping sound. Another possible issue is it could be one or more bad spark plug(s) causing the fuel to not be ignited efficiently or maybe not at all which once again could cause this sound. You mentioned the exhaust wasn’t on yet and that could mean that as there is not mufdfler on sound restriction you can hear each cylinder firing and popping. Also one more thing is to try cleaning out the carburettor with carb cleaner to ensure no deposits are restricting fuel flow,
Hope this helps! (By the way apart from the popping that engine sounds amazing :P )