If it's properly grotty, the getting a complete inner & outer sill assembly to the first floor groove is by far the easiest and best long-term solution.  I've never removed a sill and not had to do major work behind it.

If the valance has a dime size hole, just cut out the rust and weld a small patch.

When you take off the outer sills, you will uncover more rust. Take your angle grinder with cut off wheel and cut out the rust. I like the paddle switch grinder as it is far safer because of the switching mechanism. Hopefully you won't find too much rust in the inner sills but they are easy to patch. Don't overlap. Butt to Butt weld only as the lapping will rust worse.

Look closely at where the rear subframe mounting nuts are and in that area where the bulkhead is. Change out to stainless bolts and nuts.

Get yourself a hole punch and put holes spaced 1 inch apart along the lip to weld to the body. Grind smooth. Don't forget the jacking point brackets. Waxoyl if you can do it, when finished.

JM, I've been in the body shop biz since 1975. Last summer I took my Mini off the road to do inner and outter sil replacement. While I would never recommend this task to anyone with little experience, I can honestly say that the removal of old rusty bits, and installation of the nice shiny new bits, is really not any different then doing just about any American made car. If you feel like it's a task you really want to try, look up all the written and video information you can before starting this project. Just remember, the most important things, in this order, are to brace the shell accordingly, and only work one side at a time.

For detailed info on panel replacement, and problems encountered, look up MK1 mini site, register and go to forum under "our cars and projects" there is some great info there.

Thanks guys.I checked out M machine.Id imagine its fairly expensive to ship those panels from out of the U.S as im in the states?

6464 , I was never around minis so i dont know much about these cars except what ive read and done myself.I had a 998,a 1275,a disaster of clutch issues and then did the Vtec swap and flip standard length steel front.I have 0 experience on any panel replacement but the rear valance seems like a good place to start on.Are the sills really involved? They dont seem all too bad,but idk if i will uncover some hidden issues.The sills arent all that bad but i want fresh ones.Valance has a small spot about a dime size.

dido. what Alex  just said about M Mahines... ( this was a scary thought ) 

M-Machine all the way.

Better than Heritage.

JM, I did sill replacement using after market sills. What did not match up were the dents of the inner sills to the new other sills. Off a good 1 inch. You can see the mismatch, but does not affect strengh. Don't forget to get the inner jacking brackets.

I want to replace the sills and also the rear valance on my mk4 mini.What do you guys think about the aftermarket panels for these areas? I beleive they are a little thinner? Any issues with fitment on the sills?

I used the aftermarket front end parts (Wings,hood,and nose panel) on my car for the flip front and all seems well.Parts fit decent after a little massaging.