Replace panels before or after dipping?

If you insist on dipping it, at least cut away the rusty lower quarters etc so all the crud can drain out. If you don't, all the junk, dirt, bullets, bottle caps and wrenches that fell in the quarters over 50 years will still be in there. Having restored a car that was dipped, I would never do that again. It will haunt you until you sell the car. Think about a 1920's car body that's been sitting outside for decades. It will have a brown rusty surface. Metal wants to oxidize, and that's the nature of bare metal. The acid solution dissolves some of the rust between the flanges, and now you have bare metal in there, that wants to oxidize. Not to mention that it is pretty much impossible to wash away and neutralize the acid solution from all those tight overlaps and boxed sections. Formerly oxided metal between those overlaps is quite stable. The result after dipping is, it will start to rust between all the flanges again, and brown rust stains will creep out of every edge. Forever.