So let's see, the question is whether or not you should spend two days doing _something_ to the code that will make your ownership of it easier to manage?

Sounds like a no-brainer. Go for it. Of course, you'd better be sure you can really pull it off in a couple of days. Programmers are notorious for under-estimating these things. But in general, if you're going to be doing something for 2 months or more and you can do something up front that saves you ten percent or so -- do the math. Don't get into "always rewrite" or "never rewrite"

If you can recreate what they're doing that quickly, you're not that far along the development path anyway. There's a whole different answer if they've spent 3 months plugging away at it and already have paying customers. But it doesn't sound like you are there.