Take a grinder, wire brush, etc grind all of that rust off. I cleaned up my chassis way back , took it down to bare metal, used heavy coats of rust primer, then heavy coats of rustoleum rust paint, 3 years later i have a clean looking chassis still.
You shoulda seen it when i first got my hands on it hahaha! I was lucky if there was black paint on the chassis in my case... You will be alright, worst case scenario you need a lil welding and patch work.
00' 4.0L, 35's 4-5inch lift, d30 aussie locker/ d35 lsd with chromo shafts, 4.88s and an 8.8 in the progress