Rub Rail on a 3200SCR

[Mahalo]

I am attempting to reseal my rub rail. I want to remove the rub rail in sections, clean it and reseal. I am finding every other screw going thru the stainless & rubber rail is a 3 inch machine screw and not the normal 2 inch standard stainless screw. Why is there machine screws? I started this on the rear port side. Thanks.

[gmc60]

I did some of mine this spring ?
There are nuts on most of them, and the long stainless wood screws hold the boards in side boat on .(from outside yes) When the boards fall off you will see all the nuts and the top rail nuts also that leak more then rub rails from rubbing on docks and people grab it to pull you in. I did not go as far as to pulling black rubber out and taken off the base i sealed all the nuts and bolts and a few top bases 3M 4200 . All my leaks went away . So FAR

That is my short story

Bill