So it turns out sealing the gaps around the flow frames was a bad idea. The stuff I had collected was a variety of propolis and burr comb. See Gap Between Flow Frames and Metal Strip on box . So it attracted what seems to be wax moth worms.
I removed most of it with my hive tool and torched (VERY QUICKLY) the outside of the flow frames, where they meet the wood of the box. You need to be very careful to not melt the plastic. This is probably terrible advice, so don’t do it. I would not do it again, I just panicked and didn’t know what else to do to kill all the microscopic worms.
I added some more foam gasket around the front cover and put the hive on 8 adjustable feet submerged in vegetable oil to stop the ants.
There are still some straggler worms, but I have been checking every day and killing 1 or 2 each time I go out. I did a hive inspection yesterday and all is well. I actually harvested my VERY FIRST frame of honey, from the middle super, the old fashioned way. I am still waiting for my Flow Hive to fill up. They seem to be moving very slowly, from back to front, but there is progress nonetheless. It probably has about 30 pounds of honey in it, just scattered across all 6 frames, all partially completed.