TMK, I agree with Pat. Sounds like your glue was too thick. I like mine about the consistency of warm olive oil.
As far as ending up with clean glue, garbage in, garbage out. If you put a lot of nasty stuff in the pot, you'll get nasty stuff out no matter what you do to clean it. All of the sinew that goes into my glue pot is as clean as the sinew I'd use to back a bow or wrap an arrow. That way there is no fat and no meat to contaminate the glue. It ends up nearly transparent, sets solidly and quickly and is stronger than anything I've found for sale anywhere.