I finally figured out how to make the bugs move behind the clouds. It should have been just a simple change for the CTRLPF register, but I changed it and then the scanline went crazy again. So I had to fix that too. And then I had to even out the clouds and make them uniform. That took about an hour or so.
One thing, though, if the flies move behind the clouds, the fly swatter has to as well. There is no way around that. Say, changing the player1 fly swatter to a missile or something. It would still be behind the clouds.
I never dreamed that when I first got my Atari 2600 in 2005 or so, that I would become proficient enough to program something like this. I credit batari Basic (which I stayed in way too long). I can understand what certain code does, but I still don't understand the "racing the beam" thing people talk about.
I drew a fly for promotional purposes. (read: because I was bored.) I hope to get this finished. It is finished now, unless someone has a suggestion I could work in in the 138 bytes I have remaining. I wish I could get it published somewhere...