Glad it's coming along. Do you have an EGR valve on that engine? If so, try disconnecting the vacuum to it and testing for the misfire. If you added larger pistons, valves, header your vacuum will likely increase and could be causing the EGR valve to open too soon. I had to put a restrictor in mine for it to run right
Yes, it has an EGR valve. I will check it. And, the cam profile can change the vacuum.