OK, so .. having re-glued my stem plate and stripped the bit of varnish off around the spinnaker chute, I finally stopped sanding at the transom :)  so, as discussed on the other thread, I'm going to epoxy coat and then varnish it .. so far so good .. all sanded down, warm weather is here and nearly ready to get at it ... now, I removed the staining and damp damage around some screw holes where fasteners pass through the skin or into the transom, but I'd like to make sure damp doesn't get in again.  

Should I re-drill them a few mm larger, epoxy fill them and re-drill? or just use a syringe to soak neat epoxy into the hole and then drill clear again?  What about screw holes for cleats and fittings held into the wood? drill them clear, epoxy fill and then drill so the screw bites into epoxy rather than wood? or just soak the screw holes with epoxy?

Robin,

The only way to ensure that the wood doesn't get wet again and suffer from damp damage/staining is to completely seal it from the water. If you have the time, and inclination, drilling out oversize, filling with epoxy and then drilling back through the epoxy is the best way. 

Drilling normal size holes which you then fill with varnish/silicone(with its attendant drawbacks)will probably be OK until something 'works' the screw/bolt in the hole and compromises the seal originally formed by the varnish, etc. Back in the days before epoxy, a dab of varnish on the screws as they went into bare wood was as much sealing as people (including boatbuilders) did.

Soaking the holes with epoxy would be OK provided that the area beyond the edges of the newly drilled hole is sufficiently soaked that the new drilling doesn't compromise the epoxy seal. 

One option, other than the oversized holes route, would be to inject the old holes and then, just to reseal anything which the drilling might have exposed, coat the screw threads with epoxy at the time of installation.

Drill oversize to remove rotton wood & epoxy in hardwood dowels

Re-drill the holes with a bigger drill to get fresh wood, completely fill with epoxy, the re-drill at the correct size for your screw.

I tend to avoid bonding hardware because it can be a pain to get the screw out again.

For bolts through wood I over drill the hole size and coat the sides with epoxy. It can be a pain to drill the right size so that the holes size is correct after you have coated it. 

If you bond in a hardwood dowel the screw is pulling with the grain which is probably weaker in shear. If the peg is tight you may also get glue starvation and a weak bond.

How about Tufnol dowels bonded in? I'm sure I've seen it used usefully somewhere.

A little trick for getting screws out of a hole where you have coated them with epoxy when you screwed them in, is to get a soldering iron and just heat the head of the screw for a minute or so - it will screw out a treat.  If you find that some clever clogs has used a mild steel screw then the same tachnique can work but don't have a go at it with the screwdriver before you heat it.  You'll likely knacker the head and you are back to square one and reduced to drilling around it with a fine drill as a last resort.

Yes, drill out any soft/damaged wood, use epoxy well mixed with microfibres to fill, you can stick the screw in loosely while it all sets and then tighten up when it has (saves having to redrill the hole)

The above suggestion to use the hardwood dowel epoxied in was to replace the screw & not to act as a plug for a replacement screw...

If a fluted dowel is used then glue starvation is not a problem because you use more than is necessary & the excess passes up & out the flutes as the dowel is driven in. If the dowel is shorter than the depth of the hole then it can be driven in untill it is just below the plank(gently, a snug fit not tight fit)& allowing the excess glue to fill to level (maybe 0.5mm). The space below the dowel is not a problem because it is filled with epoxy.

If you think a hardwood dowel is not strong enough mock up a joint & test it to destruction. Think you will find that although a screw is stronger than the dowel the anchorage of the dowel is stronger than the anchorage of the screw.

In any event most screws in boats are to hold planks etc in place whilst the glue goes off & are not generally part of the structural strength. Having said that you have worked on the boat & must be best placed to judge that for yourself.

The places I was thinking of were the holes in the transom where the rudder pintle is bolted on for example. The wood is sound enough, but over the years even though stainless 316 hardware has been used, there is (or was, I used some oxalic acid to remove it) anoticeable black stain from iron being leached out of the fastener, and some damp in the wood.

The dowel methods mentioned don't seem appropriate, as I have sound wood anyway, its just waterproofing I am seeking to achieve, so I'll drill oversize by a couple of mm, soak the holes with epoxy, then pack it with an epeoxy filler mix and re-drill. 

Thanks for the advice. Wish me luck, tomorrow the two coats of resin go on.

Ah! a misunderstanding of the question...

OK so if you are looking to improve the security of your pintals or high load fittings then epoxy will do the trick

1) If you are happy with the anchorage then as you say neat epoxy will soak into the wood sealing it to to water ingress.
2) If you are not happy with the anchorage then overdrill the hole by quite a large margin, soak timber with neat epoxy remove the excess & fill with WEST mixed with their filler produced especially for this purpose (Forget its ref number). When hardened off this can be drilled & tapped but be careful use a coarse thread & take it slowly in my experience whilst very strong it does not like any heat build up. Instead of using epoxy/filler one can epoxy in a plug of a tougher material Tuffnal, plastic, metal or a harderwood. The key is to spread the load so bigger gives a bigger gluing area (so better spreading the load) & is also easier to work with.
3)For through bolting either neat epoxy to seal the timber & drill through to clean out hole as you suggest or overdrill by quite a large margin soak timber with neat epoxy & fill with a mixture of WEST & suitable filler (hard) then when gone off drill through leaving an epoxy/filler tube around the bolt

If you are worried about changing the precise location of any fitting particularly the rudder fittings do one hole at a time using the fitting located with the original fasteners as a jig. I use the Brad wood point drill bits ie the ones with very sharp points & a  lightweight drill stand G-clamped to the transom. Time consuming but quicker than making a mistake...