So... I think I found the source of all my endless metal pieces. To make a long story short, they were coming from the flush canister! Everytime I'd unscrew the top to pour in more flush the brass fitting was cutting the aluminum flush bottle threads. So hence, endless metal showing up. After cleaning everything out i devised a new way to get flush in, use the vacuum pump to pull it into the flush bottle. I think i probably destroyed my vacuum pump though as i accidently got some flush in it. Anyway, now im flushing the system by reusing the same flush over and over by filtering it. I've got it down to almost perfectly clean, probably a couple more days to get it perfect though. If my bottle has been doing this all along that's probably what took out my new pump too.
So beware of the flush bottle if you ever use one! It's like being betrayed by your best friend who is supposed to be helping you, but then BAM, stabbed in the back!