Holeykeman,
Soaking the bolts with penetrating oil should work. Also, if you have a small LP.MAP gas torch (for soldering pipes) you can use that to heat the bolts and that thermal shock should release the rust bond.
You should be able to pry the J-nuts out buy you may destroy them and have to replace them, but they are not expensive (don't buy them from Ford...see my replay to Bo below).
Bo,
If you managed to get one bolt out in one piece, you can take it to most hardware stores and get replacement bolts. They are metric and I think they are either 6mm or 8mm in standard thread pitch. The harder part is getting the J-nuts that hold the step bar mounting brackets to the lip on lower part of the body where the holes are not threaded.
Many years ago I purchased a used set of step bars (my 2001 ST did not have step bars), but the guy did not have all the bolts and J-nuts. The odd part was that my new ST had a few J-nuts installed even though my ST never had the step bars??? Anyway, I could not find any J-Nuts locally and ended up buying a box of 25 J-Nuts on the Internet along with all new bolts. I think the whole box of 25 J-nuts was only about $6-$7 compared to some places that wanted over a dollar a piece for them?? Once you know the metric bolt size and thread pitch you can order the J-Nuts.
I had my step bars painted red to match my ST and the shop clear-coated the curved front and rear pieces with a special StoneGuard clear-coat to prevent them from chipping....It worked great.
...Rich