My Street Demon install experience

So I was doing some tuning and the car began to run like a dog and would barely idle. I pulled all the plugs and they looked great so I changed the fuel filter and drained it into a cup and..... uh oh.... this aint good. So I bought some clear filters so I can monitor the situation. They were less than $4 a piece. I'm guessing the tank needs to be changed but I'm wondering if I can just filter the crap out of it after a few tanks of gas????