Going to guess you never solved your centres correctly to begin with.somehow, the centers swap positions after I'm finished pairing the edges. Maybe it's because I use Dw R' F R F' R U' R' for the last two edges? Not sure.
Sort of, but to repeat what others have said, learning the Yau method is recommended. Yau is somewhat less efficient than (the most efficient variants of) reduction, but allows for much better piece visibility and lookahead.Also is it viable to do centers first then edges?