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Unless you have it dip coated there isnt much you can do without drilling lots of holes and installing a spray wand. Most rides that have boxed frame rails arent driven in inclement weather anyway, at least here in the rot belt. In LA I doubt if it would ever be a problem.
If I were boxing mine, I would consider spraying the inside space with a 'weld through' primer then maybe pull a wad of cotton wrags through it that has been soaked with zero rust. Anything will be better than nothing.
Paint stores and Eastwood Co. sell a product called Cavity wax, you can use the wand (already mentioned) to spray inside. That's what I plan to use on my Corvette. I have also heard of old motor oil being used. Messy I know, but I guess it does the trick.
My boxing plates, front and rear were not too long to prevent me from dabbing with a long chip brush from the ends, I used a rust converter, then spray can primer that I sprayed very heavy. I think the pulling a rag soaked with rust converter sounds like a great idea.
the weed sprayer thing is a good idea, if you have boxed the entire frame, extend the spraywand with steel brake line and you can shove it into the frame from the rear of the rail and spray it all from front to back good luck
Ive thinned ZR about 30% and had excellent results thru a 1.0mm HVLP detail gun nozzle. What is the extent of the boxing? If its not more than the firewall foreward then get a case of beer and some friends to stand that thing up and spray. Gravity is useful at times.