what's this russian steel that defies metallurgical properties by being an alloy too?
sorry couldnt resist.
your key to getting this right, is the right approach. forget about trying to minimise paint damage or try cut corners. What ever is required to get at the rust, do it, no matter how much paint you have to feather back., or how many holes you have to punch through. dont be tempted to leave overly thin corroded steel behind, just cut it out, and get rid.
heres all the advise I can give you. hope it helps you.
Get yourself some 3M scotch bright rotary discs of various grades to take off the surface rust on the rcovearble areas. DONT USE EMERY ABRASIVE PADS IN A DRILL!!, you will take too much metal off in one go. the 3m pads allow you to take off a little at a time and asess if you want to go deeper. for the window channels, a steel rotary high speed wheel is best, it will get into all the gaps. take ALL of the paint off in there. grit blasting is just too damned messy for my liking, you will be vacuming it out of the car forever!
Any steel that has pitted deeper than a few microns into the steel, clean off as much as you can with a wire rotary, but not all of it, you need to leave some traces behind on the pitted areas for the POR15 or phosphoric solution to react with and stabilise a base. if you apply any phosphoric solution like POR to clean metal it will introduce corrosion by strpping the steel of any protection at all, it will go orange surface rust within 30 minutes, It needs a small amount of ferrous oxydation to do its job (it should tell you that anyway on the tin). use a product like POR15 or similar that leaves a very hard converted oxygen impervious base behind (normally black) that can be painted on top of.
Dont bother with your local wall mart rust coverter rubbish, it wont cut it, as they are not allowed to sell industrial strength stuff to the general public, just in case you are retarded enough to spread it all over your face or eat it!
If you can get neat phosphoric acid or hydrochloric acid 70-90% concentrate, this will kill the rust with a few applications, but will also strip the metal of any inherant protection, so you will need to put a stabiliser on afterward (within minutes of being dry). let it dry, then put an acid zinc etch coat on asap. try use an acid etch that isnt hygroscopic (doesnt absorp water), otherwise you will be forced to primer within 4 hours of etching too.
Other excellent products for killing the rust are made by Dinitrol. there are some awsome products they sell for oil rig uprights. if it can handle Atlantic salt, the alfa is no bother.
remember it doesnt need to be pretty in the window channels, your aim is to stop the corrosion dead in there, so if you cant get a smooth paint finish in there, who gives a rats arse, no one will see it. when you put screens back in, a good trick is to smear aviation jointing compound between the inner seal and metal channel, it will stop moisture being held against the metal. (the most common brand is Mastinox. Its a yellow stuff that sticks everywhere!!)
The only other thing I would say to be aware of is Mechanics!! if you have any welding done by mechanics, they WILL, no matter how good they say they are, cut corners if they have a boss, deadlines and a body shop full of cars, period! find a resto expert not a general body shop! make sure they etch both sides of any plates they are going to weld in, with weld through etch primer. INSIST ON IT, otherwise the new metal work will start rusting within weeks of a new repair, which makes the whole repair pointless. also ask mechanic what gauge of welding wire he is going to use, and insist on short small spot welding cycles, to avoid heaps of body filler having to be applied afterwards. to do it right you really need to pull the entire dash, so that paint can be applied both sides. heat soak from welding outside, even in short cycles will damage paint on the inside of the car, but you could always cheat a bit and just squirt ACF50 corossion inhibitor along between the dash and bulkhead before screen refit, that should track along the bulkhead and stop anything before it starts.