Should I wait a week or* two to let the epoxy fully cure, that is.

I go for a 24-hour cure (normal temps) before the second drilling.

For padeyes, I've taken to rolling up a scrap of glass cloth, saturating it with epoxy and pushing it into the screw hole. It gives the threads something more substantial to grip than epoxy. It's especially useful when repairing a hole where the screw threads have pulled out and shredded the wood.

Laszlo

Thank you, Laszlo. Now that you mention it, I remember seeing the bit about fiberglass on your blog. Do you remove deck fittings like padeyes when you are refreshing the varnish or simply work around them? Guessing the latter. Given that the padeye will be my anchor point for the stern cartopping tie down, I would hate to back the screws out even once after bedding them and weaken the attachment.

I take them off. The epoxy is for waterproofing, the glass/epoxy is for providing something for the screws to bite into. For bedding there's silicone compounds.

Laszlo

Well here's a first. Laszlo and I don't agree. Wow, that's never happened before.

I hate the redrill portion of drill fill drill. I never seem to get the second drilling centered in the original hole. And it requires a frustrating day of waiting. I often will let the epoxy cure around whatever is going to ultimately go in the hole. If I'm worried about release, I rub a little candle wax on the object or use mould release. If the epoxy grabs a fastener I apply some heat directly to the object in the form of a soldering iron then back it out. An impact driver carefully applied can be your friend by that tapping impact. You can also break the head off of your fastener if you're not careful. That is a TOTAL pita.
One does have to be careful to make sure what ever object you’re putting in the hole stays centered in the hole! Painters tape or some creative jigging has worked in the past.

i was reading this and thought there were some interesting perspectives and that i could add something.  first, we probably should have started with the question. what kind of screw were you going to use to attach the padeye?

fwiw, i only drill, fill, drill when i am using a machine bolt (e.g., a bolt that's going through the hull that is going to get backed by a washer/nut. 

if i am going to be working with a wood screw into a block of wood, i drill the hole in the wood approriate for the wood screw, put the wood screw in, back it out, fill the hole with epoxy and then wood screw in and back it out....and then let it cure.     when the final wood screw goes i, silicone on the screw.

for my drill/fill/drill machine screw technique i look for at least a 1/8 inch 'rim'.  so a final hole is always a 1/4 inch more than the target.  i agree that centering it can be a pain.  i handle that by doing a pilot hole for the final hole with a finish nail or 1/32 bit....which is fairly easy to center...then follow it up with the actual bit for the final hole.

anyway, i hope that is helpful.  

h

Really appreciate the detailed replies. I need to take some time to digest them, but to answer hspira's question, I was planning to use #8 x 3/4" or 5/8" silicon bronze wood screws only because that's what CLC seemed to recommend along with the padeye. It seems like a machine screw or a through bolt might be better in terms of mechanical strength, though. I backed that part of the kayak deck (4 inches in front of the stern) with an inch or so of thickened epoxy as recommended in the manual (I think). I'm mostly interested in strength (of the padeye connection) rather than the ability to remove the fasteners later. Usage will be mostly in fresh water but also in sea water a few times a year, but I will store the kayak in an attached garage.