It looks like the engine RPM is moving around a little, thus the change isn Hz and voltage. Everything else looks to be good.
For now I have update the inverter to just use the generator as dirty input and not attempt to sync with it.
Thus when the generator is running loads will be limited to the generators max VA. With my little Honda EU2000i and the auto transformer (stepped the 120 to split phase 120/240) I was able to sync the two, thus I was limited to peaks of the Honda +16.97kVA which was great.
I am going to see about getting some diesel injection cleaner add it to the fuel. I will let the MEP-802a do it's weekly tests and run through a few power outages to see if it smooths out. If it becomes more stable (It's really good enough for everything but my inverter to sync to it) I will attempt to see about putting it back into support mode and give it a test.
For now things seem to work well enough, my well and other normal loads work off the generator, if the loads are too big the inverter will temporarily drop the generator and run from battery and with the generator when it's dark it should only need to run for 1 hour on and 5 hours off. I am likely overthinking things and have a really good setup (perfect does get in the way of good).
Thanks again!