Checking my guide, you would only have received Phoenix if you gave FuSoYa at least 2 Augments before you fought the CPU.

The key with the save points is knowing how to backtrack to the two that are available. Also, the best advice I can give for Behemoths is to cast Blink and Protect on the boys and have them lay smackdown physically, and don't bother with spells because Behemoths have a wretched spell counter.