Rust prevention for troughs

I did this on mine. They were in good shape still galvanized! I had the fenders off and had to remove them to get to the cowl. (Inside of my cowl was swiss cheese) I lightly sand blasted them, welded them back on and applied spi epoxy followed by restoration shop 2k urethane (under hood black) recaulked with brushable seam sealer and replaced the rubber seals. I don't expect problems for the rest of my lifetime. 

Don't forget to paint/treat the underside of the front fenders above the troughs.

Back in the early 80's, long before POR15 and other corrosion prevention products, my brother-in-law and I used a mixture of STP (remember that?) and mobile home roof coating inside the fenders and troughs of my then-wife's 72 Javelin SST. Also put it inside doors, trunk drop-off areas and anywhere else midwest rust was likely to attack. My daughter still owns the car today, the body looks great, even tho it's been driven in salt/chloride winters in Illinois til about 10 years ago when she moved to Texas. Unfortunately, the floors, trunk, frame rails and other areas we didn't treat or couldn't easily get to are toast, but the fenders and doors still look great.
  If it's going to be maintained with any sort of concern for the elements, any etching epoxy primer and top coat will do. Even brushable Rustoleam would be a good choice for the trough areas. Remember, these areas were either dipped in primer or missed entirely when the cars were new and they weren't expected to last 50 years! A side effect of the STP/roof coating mix was that the car would "leak" from the doors and bottoms of the fenders during hot summer days. Paint it with something and let your heirs worry about it for the next 50 years.

I would like to second the comment about cleaning and protecting the under side of the fenders. My 1970 had the tops of both fenders soft and rusting through when I got it. Funnily enough, the troughs underneath are fine, to this day. The water and sand and all that collected but the corrosion did not seem to harm the troughs themselves. Worst thing that happened to them was that the staples holding the rubber seals on rusted away!