So I know third party bases aren't tournament legal but what about keeping the base but making modifications to the rods themselves? I've been kicking around the idea of going with metal rods and only modding the base so I can attach the metal rod. My big ships' pegs keep breaking on me.

I don't see why not, it wouldn't adversely affect anything that would matter gameplay-wise.

I think that technically it's not allowed - except for maneuver and range templates, everything is required to have come from an FFG box and be unmodified (except for ship repaints). That said, I have a very hard time seeing any TO take exception to this.