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I occassionally drilled a little deeper into the 1"x2" board and used a cleco to temporarily secure things.
One of my concerns leading into drilling these holes was how to secure the stringer where it butts against the forward longeron. If you remember, I chose to do my splice differently than the plans call for. I'm doing this splice from the outside with screws instead of the inside with consunk rivets. So, at this point I have to undo my splice to drill my holes. This means that nothing is holding the two peices together where the stringer butts against the forward longeron. So, I carefully held the stringer and skin in place with a clamp and twisted it inward (because the top skin wants to bow outward) until everything lined up and then drill the first hole nearest my splice and installed a cleco. I also used a couple of wood clamps after this first hole was drilled to twist everything into alignment. This really wasn't as hard has it sounds. Just take care and drill that first hole carefully. Everything else falls into place after that.
So, once all the holes are drilled, you can remove the clecos from the underside, loosen the straps and clamps carefully and install clecos on the outside. It is one of those times you can look at your project and see that you have accomplished something of significance.
By this time, the turkey was done and I had one more thing to be thankful for!