I test ran the engine again today. With the 16-8 rpm dropped to 7000. It seems like I lost some torque with the increased duration. Also, the ring needs to seat more. I put the 16-6 back on and ran the engine at about 3500-4000 rpm for about 30 mins. I then tested full throttle again, and rpms were up to 7800. I think most of that improvement was from the exhaust modification. I let the engine run for about an hour total today at low throttle (mainly to keep the heat down) and on my last rpm check, I was getting 7998rpm! I think with a bit more run time, I will have got the 8000 rpm that I want.
I have decided to leave the transfer ports alone, and am going to run the engine as is. I got the target power that I need. Once I can afford it, Im going to order an XYZ CDI for this engine. I think that rpms should increase as well, cause the heavy flywheel wont be holding it back. I also still need to get a header pipe made up, and a velocity stack. That probably wont happen for a week or two.
For now, Im going to modify one of the other cases for EI use and get one of the flywheels center cut out.