If you have "split" documents (one male, one female) and are filling out a FAFSA, that could be enough to flag you as male. Are you registered as male with the school?
I'm with Devlyn Marie. Fill out the form and see what happens. Worst case, SSS does check you in the SSA database and kicks you out of the SSS system because you're not legally male with the feds. Best case, registering now could save you hassles later. The only way to find out is to do it.