Thanks everyone for your responses. I must admit that I didn't get much sleep last night thinking about this problem! Here are some pictures to help explain the dilemma.
The fuselage frame has been riveted together and the first 4 skins are drilled and clecoed on.
Before skinning I checked the frame for straightness and the keel of the canoe is dead straight within 0.020 or less.
Both of the fuselage sides between the tail end and the back of the baggage compartment bow out slightly by about 1/8".
When I try to get the side skin pulled in against the fuselage side and bottom it does not sit flat along the bottom and the wrapped over portion ripples up. This ripple moves around depending on where you push and it is impossible to get it to go away.
The problem seems to be caused by the sides bowing out. It is a very slight bow so it is not noticeable in the picture however a stringline shows that the bulkhead side flanges are not in the same line.
On the inside the bulkhead is being distorted by attempting to pull in the skin to get it to lay flat. This makes me think that bulkhead F-607 is too wide. Or maybe F-606 is too narrow. I also noticed on Sam Buchanan's website that he had to split a bulkhead and make it wider.
It's quite difficult to measure the bulkheads against what the plans specify on Drawing 24 but this is what I'm trying to do now.