As to the OP and the POR references and all the current work, harz, spudman, etc., I am currently reduxin my gutters. Started with the FAQ, which btw is

great. So, I found the very beginnings of what yall are dealing with in my gutters. But, being as I would like to avoid what you have on your hands I delved into POR. It is intended to eliminate the occurence/recurrence of rust, though preparation is the key according to the "non"-directions below. The Marine Clean & Metal-Prep solutions are quite a bit cheaper than the POR itself, $9/4oz., $30/pint, $50/qt. 4oz. is about 10sq/ft. @ 1 coat. Clean, Prep, POR a few coats, rough the final coat, primer/paint, rough, seam sealant, prime/paint/clear. But from what I can tell, which may be worth nothing, POR looks like the right stuff if you love your cruiser and you don't want to do it again. I mean, no one gets out alive, right? Just sayin'.
Check out the "Directions for people that don't read directions" and the explaination about steel manufacture that should raise any eyebrow:
qr.absolutecoatings.com/QR-assets/.../POR15/POR-NoReadDirections.pdf
And, the 3M Urethane Seam Sealer listed in the FAQ is also available in a 1/10 gallon tube that fits a standard caulk gun and is considered an OEM replacement. There are also 3M pads of varying grits for cleaning/scuffing prior to application that are specifically called for. I picked up a 4"×6"pad for $5 @ NAPA that will do all the seams I know about on he truck. Also a great pad for cleaning gasket surfaces.
Btw, props to ya harz and spudman for taking it on, its bigger than it looks. Way bigger.
Harz, if you have all that rust up there on top, then where did the salt-laden moisture that caused your problem, and has consequently continued to drain into the cruiser, go? Are your floorboards, rockers panels, and/or pillars compromised? Looks like some DEEP inventory should be taken there, eh?. Have you pulled up the carpet or removed the inner trim verticals to see behind and verify the structural sanctity of the upper chassis, and not just the roof? But, hey, a good welder can change the world, right?

C