Sorry for the delayed response. One thing I left out is that I recently bought a Composite/S-video mod kit from Winz_mod. I've been chatting with the group on discord. It seems that one of their latest boards that they've been selling recently shorts out and results with the issues I am having.
The troubleshooting method that Stephen recommended would have worked to eventually point the finger at the mod board.
I hooked up the Atari with RF and the system still works, thankfully.
Thanks for all the input, guys.
Hopefully I can successfully mod this system with nicer outputs, but until then I'll have to play Atari today in full "retro mode".