If your megafuse was blown, it would illuminate the charging light at all times.
The FUSE itself if fine.
The possible problems could be:
battery
alternator
wiring from the alternator to the megafuse
wiring from the alternator to the chassis
wiring from the battery to the megafuse
wiring from the battery to the chassis
You've eliminated the battery, so look in to loose wiring at the actual mega fuse location (both side of the fuse), and check your battery ground, and alternator/chassis ground.
otherwise, the alternator could be toast/going bad.
