I just want to say thank you to everyone that has helped me, @Jason Carr included. You all have been very helpful and quick with replies. Thank you!!!
I have figured out a ton of issues on systems, thanks to your help and @SentaiBrad's great tutorials, and now I just have a few that need to be ironed out. The ones that I mentioned in this thread. Now I know that I can't really run PS2...still have issues with Dreamcast and Saturn but we're getting there.
I will try the steps again about my issue and will get back to you all when I get a chance.