It's risky in the absence of automated tests. Of course you'll test as you go along, but that's tedious, and error-prone. Ideally you'd write unit tests capturing the current behaviour, but that's not always feasible.
Having been in this position before (with PHP), if the code really stinks, refactor it very slowly and very carefully.
I think your plan's sound - take the long method, break it up with whitespace into paragraphs, and try Extract Method. Quite how you do that depends on how many variables are in play, and how they interact. Try trace the dependencies of a paragraph before you start.
Is it worth it? If the code's really awful, and its awfulness is starting to spread, then it's time to get stuck in there. If it's been running fine for ages, then you risk introducing bugs into something that for now Just Works.