Any chance you can automate the reformatting somehow?

Even if you could just put in a "table starts here"/"table stops here" type of marker around the tables, then the rest of your problem gets a lot simpler.

Given the number of tables you're dealing with, I agree that's probably not trivial. But if you're lucky, there's some indicator you can "grab on to" to start from. How are the tables declared, with [][][]...?

I think there's got to be a way to get a start on the problem, but without knowing what the code looks like, it's hard to make intelligent guesses.