Ouch. OK, you've got "moderator" after your name so I guess that means my first thought is out: You're not swiping someone else's site wholesale :) And the second thing I was going to say was that query strings aren't in the URL, they're... Well, holy smokes. They're in the URL. But the format is consistent, so things are not so bad.
Either that or keep the original file names, and somehow use code to tell the server to serve these pages as html file types.
And that's the good news in a nutshell. You have been handed a priceless opportunity to hammer all names into the exact form you want. Global renaming offline is not an issue. I do it with-- of all things!-- a graphics program, but there have got to be other ways to deal with it.
:: detour to Forums Search ::
Post # 4434258 [webmasterworld.com] to be exact (second reply in thread). Read and assimilate.
Now, you don't have armies of customers pounding on the door wanting the site to be up and running yesterday, do you? Take the time you need to decide exactly what you want the names to look like. mod_rewrite does not lend itself really well to temporary fixes that you're planning to change next month. (Well. Actually the rewrite itself is not hard. But the googlebot never forgets. You can finish the thought yourself.)
Oh, and by absolutely amazing coincidence there's a post about Server Side Includes (can I assume you didn't mean Supplemental Security Income?) within the last couple of weeks in this very forum. I don't care for the line "If I can do it, anyone can" -- but I don't speak php and am deathly afraid of Terminal and nevertheless managed to get it done. So there you are.