On my wood duckling, I just drilled out any holes I needed to.

Try everything that works. Shrink wrap where you can, duct tape where it works, and drill new holes for wires where you need to pull it tight. I've also found that nylon strapping with ratchet clamps works well on especially difficult spots. -Wes

I used clear plastic packing tape (stretch wrap would be fine also) exclusively, no wires on my Shearwater 14 and also my Wood Duck.  Two people for this job is a big help - one to hold and the other to tape/wrap.  Use a putty knife to slip in the crack between hull and deck to pry the appropriate piece in or out to line them up when you get to tricky parts.  The bevel on the hull and deck edges helps to hold them in place once you get them lined up and taped.  Then I went right to the fillet/fiberglass tape step with no tack welding.  Worked fine.

If there are any small gaps on the outside seam when you're done you can just fill them with fillet mixture and by the time you're done with sanding to round the edge and fiberglassing it's not very noticeable (at least no one ever noticed it on my boats). 

I would have to agree. The instructions are not very clear....On my SW 17 I redrilled a few holes on each side where the deck needed a little help to meet the hull nicely. Then I used shrink wrap on the rest (and a buddy to pull the edges together) It takes some time to get everything lined up but the more time you spend now will be less time filing and sanding later and a much nicer looking end result in my opinion. The holes you redrill will be filled again by the fillet and tape. I am about a month away from finishing mine :^) got the final layers of glass on the hull and sanded now for the deck!

Well, I used the stretch packing tape well and it only worked with my wife as an extra hand. I tell you, this is really a two person project for many of the steps to go well.

My new problems is that during the fiberglass connection process while the boat is on its side, I have had numerous problems. I cant really see if the epoxy filler was spreadout well and if the tape was rolled out nicely. When I rolled the boat to seal up the other side and the area around the bulkheads, the first fiberglass tape starting moving and coming off the joint. Needless to say I had to go back and fix the first side tape and joints again and just left one side done for the day.

Instructions speak to this part as being easy and relatively quick, but it has been a pain and I feel that its quality will be poor. Anyone else have issues at this part?

You've already discovered that you have to let one side cure before you can do the other side. Don't be concerned about the smoothness of the fillet or tape. As long as it covers the seam it's okay.

One trick I used to check my work is taking photos with a small digital camera that can be held and operated with one hand. -Wes

I disagree with any instructions that say this part is "easy and relatively quick"  It's always the worst, most messy, leaves-you-feeling-like-you-didn't-do-a-good-job part of any build I've done. You can't see what you're doing, and you get epoxy everywhere (I wear a shower cap as well as the normal long sleeves, gloves, etc.).  I alwalys tell myself that no one is going to be sticking their head in the hatches and looking around to see how messy it is, and it's not like the boat is going to come apart if it's not perfect. 

Definitely do one side, let cure for several hours (overnight is best) then do the other side. 

I agree with KathyD that this is the messiest and most unpleasant part of building a kayak. I now use a caulking gun to install the fillet. West sells empty shells that fit any caulking gun and can be reused. You can also get shoulder length disposable gloves from farm supply outlets, but don't ask about their intended use. -Wes