Hi Scott.
I have a 64 230 SL and have replaced the outer wheelhouse with the outer fender in tact.
I mig welded the wheelhouse, first tac welding the vertical seams in the join at the centre of the wheel space, then welding the entire join front to back, painted the car, stone guard and more paint.
The joint sealer I have used when replacing the floors and other panels,BUT, always poured fish oil into the seams (panel laps) at the end of the exercise.It is the reason I believe my car will be rust free in another 50 yrs.
I found a rubber gasket in there as well. No idea why.
The drain holes for the channel that houses the seal for the soft top lid dump water into your problem area.Bad idea.
I have drilled numerous 19 mm holes into all closed box sections for spraying fish oil (which can be repeated) and sealed them with rubber blanking plugs, and screwed in self tappers at the low points to drain excess oil.
I,ve used stainless screws on rebuilding the car and dipped every screw bolt in fish oil before fixing . This lubricates the thread, seals the thread, when dry acts as a Loctite, prevents rust,and guarantees you will always be able to undo the bolt.
Cheers,
Mike.
Feb 64 230 SL RHD Auto .Both Tops.