Congrats, it sounds like your pond is coming along nicely. With all that FHM fry swimming around, your bass should grow quite fast!
The first thing that comes to mind on the comments you made about the fish you caught is that FHM do not grow to 5". If you catch anymore that size, try to get a photo and post it on here.
As far as the fish in the mud hole going up from your pond or vice versa, I think both are possible. The bullheads probably were present in the mud hole for years and decided to swim down stream and call your bigger pond home along with the GSF. I wouldn't stress out about the bullheads. The bass will grow fast and start feeding on them.
As far as seining the smaller pond, I think it is probably going to just be a drop in the bucket...
