Wow, your stock RF is horrible -- much worse than the typical console I get here. You should be able to get it to look better than that, for a fair comparison. Perhaps a replacement cable and/or switchbox (if you're using one), and a few tweaks to the adjustable chokes are needed. If you have a frequency meter, the FSM tells you what values to tune for.
I just took the Atari I was modding and plugged it into the TV with one of the adapters. Granted it is a LCD which typically exaggerate any imperfection in the signals. If I still had the Ataris I would adjust them but they are shipped off to there respectful owners. On the 2600 comparison I will send you a PM for help in adjusting the signal.
Thanks for the files, as it forced me to upgrade Eagle to open them, and I found that Eagle 5 is so much nicer!
It looks great except for one little thing - you've got a surface mount component on the board, which makes it so I cannot actually build one of these.
I realize it's a very important component that is not available in a through-hole package, but it does beg the question: if you have one SMT device, you might as well make the whole board SMT and have them assembled, as most of us cannot actually solder SMT so it doesn't make much sense to sell a board that we can only make 95% complete. That is, unless you are a soldering wizard and will sell the boards with the SMT device already on.
The SMT chip is a SOIC-8 which isn't that bad to solder. Making the entire board SMT would be a lot worse for me and you to solder. I could offer to have that one chip presoldered on as it only takes a minute to do.
I still have to clean up the boards silk screen as it would be very hard to read all that mess.