I'm not legally male yet so I can't answer your questions. However, I plan to apply once I legally change my federal (social security) gender marker.
I'm sure you're aware that ftms ("those who are born female and have had a sex change", according to the selective service FAQ) are not required to register. All federal jobs, that I know of, have three questions that go something like this:
a. Are you a [legal] male born after December 31, 1959? yes no If no, skip parts b and c.
b. Have you registered with the Selective Service System? yes no If no, go to c.
c. If 'no', describe your reason(s) in item #n.
If push comes to shove, answer yes, no, and then explain your situation: persons assigned female at birth are not required to register and you've applied for your SIL. It may or may not work for you. When I did my paperwork for the government position I was "applying" for (hospital clinicals), they were all very understanding and helped me fill everything out appropriately despite it being a rural area.
Feel free to ignore me if you know all of this already or if you are completely stealth.