Garrett,
Like Bill says, do one side at a time. I can't stress enough the need to soak your body bolts/cage nuts. Patience is the operative word here. I would strongly recommend soaking every other day for a week before even trying to remove the bolts.
I'm not entirely sure that drilling holes to squirt penentrant is necessary. I was able to "lubricate" all of the body bolts/nuts on my '70 Elky by simply utilizing various holes in the frame. I had 100% success in removing all of my bolts with no incidents and it's not a California or desert car so rust was definitely a factor.
There's been a ton of stuff written on the subject (too much, actually) so don't be shy about doing a search. You'll find lots of opinions about how to go about it but the bottom line is simply where your own comfort level is.
My recommendation would be to remove your bolts the same way you would use a thread tap to clear metal chips as you tap a hole - only just the opposite. Apply enough pressure to just get your bolt started. No more that 1/8th of a revolution. Then screw the bolt back in slightly and repeat the process. By working each bolt back and forth, you're removing the rust that has built up on the end of the bolt a little bit at a time - which has to pass through the cage nut in order to be removed. If you take your time and have patience, your chance of success of not breaking loose a cage nut will be much, much greater. It's time consuming but it sure beats snapping off a bolt or breaking loose a cage nut.
Good luck and let us know how you make out.
p.s.: Don't, repeat don't, open either of your doors while you have your car jacked up and are doing your bushing swap.
Rich