Well, well, it looks a lot like the repair I'm doing as we speech, except I'm doing the LHS.
http://www.311s.org/phpBB2/viewtopic.php?t=7759
Take note of what panels go where and just re-build it from the inside out
That rust on the inside of the pillar does look awful but it is only surface rust.
If it is badly pitted and in your opinion lacking in strength, then more surgery is required until you are back to decent thickness metal.
You can try shoving a wire brush up inside to clean it up as best you can.
Providing the metal is sound, I would repair the rust outs and at the appropriate time, squirt a dose of Cavity Wax inside all the boxed in areas.
That is what I intend to do with mine.
You might need to drill a few access holes but they will be hidden ultimately.
It just isn't practical to clean all those inside surfaces back to shiny metal
Even using zinc annealed sheet is not the answer because any decent amount of heat will destroy the zinc surface.
Spot welding is the only way to avoid that problem and one of those is not normally a type of welder one has in the home shop

Make sure you create some drain holes in the base of the "A" pillar.

They are necessary to allow condensation to drain from the box.
You're on the right track, makes the possibility of a 'glass repair a bit out of the question, doesn't it
