The crab legs option card lets me play 2 cards in one register. If I have 4 damage, this leaves me with no cards to play in the 5th register. Is this just a pass in that turn?
Unfortunately the rules don't quite say this explicitly, but the intent is that you must have a card in every register. If you only have 5 cards, then in order to satisfy that you have to put one on each register, meaning you can't use crab legs.
There are a few things in the rules that at least strongly imply that. The biggest one is the "reveal program cards" step, which says "Each player reveals his or her Program card for that register at the same time." That doesn't make much sense if a register can be empty. The instructions for placing your program cards also seem to assume you're putting one on each register.