[quote=down_shift]
What is the best method of 1) cleaning the non-slip areas around the foot print of the handrails (removing 25 years of debris and varnish/Sikkens buildup) and 2) reinstalling the handrail?  Would covering the bases of the handrails with butyl tape (aka - Maine Sail) be the best solution?  I am worried that his tape would be too thick and not compress. 
 ... While the holes through the deck are open, should these be coated with epoxy then redrilled?[/quote]

I wish I could give you an answer for question #1.  I've got the same issue, and have managed to clean off only some of that stuff with a combination of scraping, wire brushing, and even a dremel tool.  Best not to make a mess there in the first place (One tip: do not leave varnish-soaked painters tape on the non-skip for months over the winter -- don't ask me how I know!).

As to question #2, I've been using butyl tape (from MaineSail) to do all above-waterline rebedding for the past few years, and one thing I can tell you is that you definitely need not worry about it not compressing.  Indeed, that stuff will continue compressing for many months after you install it (and thus continue to very slowly bleed out the sides for months if you've used too much), so the trick is not to overdo it.  That said, I would think it to be the best choice.  Its not messy to apply like other materials, and allows for easy removal or resetting.  It helps if you champher the top of the screw holes in the cabin roof to hold a small bead of butyl that you will wrap around the screw.

As to epoxying the holes, it depends on whether these is wood core in that area.  On our 1985 Mk I I've yet to encounter wood core anywhere in the cabin roof  -- either where there were existing holes or where I've added them (including a rather large one I cut to install a vent fan).  I'm not saying there is none -- I don't know (documentation I've seen for models later than mine seems to indicate wood core in the cabin roof in some areas) -- just that I haven't encountered it.