Jenny, here's my shot at a few of the issues you raise.

"I had considered the Mill Creek 15 but CLC's catalogue says it's harder to build."

Well, I'd trust CLC on that. I can say that I had no prior experience building much of anything, and I built a 13 that I both enjoyed building and that turned out well. I would add that I have always had a mechanical/do-it-yourself bent, so it was a gratifying challenge. If you have the basic drive to build any of these models, you can do a Mill Creek. If you decide to do it, I'll be happy to explain what I used to get through planing the shear clamps (preview: I used a small, $14 swedish plane available through wood specialty stores that was a breeze to use right out of the box, which is nothing I can say of regular planes). You will also want a good saber saw and some patience to cut off the excess deck and then plane it again. Those are the only more challenging parts of the building process that I can think of. I found those parts of the building process to be challenging, but surmoutable.

"The Swifty I have now is rock solid stable (which I like) but is
soooo slow. I don't need a fast boat but the Swifty takes hours to get
anywhere."

The Mill Creek is not as fast as a long, narrow touring kayak, plain and simple. So much depends on how much faster you want it. Can't speak to how much faster a Mill Creek would be than the Swifty, but I'm guessing faster enough to make a difference. I checked the specs and it looks like the Swify is a few pounds heaver, about the same in the beam, but 9.5 ft long, compared to possibly 15 (if you go with the longer Mill Creek, which sounds like the best of the two for you). That's quite a length increase. The gain in wet water line would have to make a noticeable difference. Still, your best speed gain would be with a touring kayak.

"I do get uncomforable paddling my Swifty which I think is more positional than
anything. My feet are so far apart (it's about 33" wide) that my hips
and lower back start to ache. There's not much seat adjustment that I can do to fix that either. Stopping and straightening my legs out directly in front
of me alleviates the discomfort. How is the Mill Creek's slatted seat?"

The slatted seat is surprisingly comfortable. CLC urged me to try it before trying some other seat. I did and I've stuck with it. Several "guests" of all shapes and sizes have found it comfortable as well. BUT, I've never spent more than a couple of hours at time on it, and I doubt it would be comfortable for an all day paddle. I think the best option for you would be to make your own from foam, or buy the Creature Comfort seat from CLC. I have two of them and have spent long hours in them. They are very adjustable, fit many different sized/shaped people well, and (IMHO) are worth the somewhat high price tag. I may eventually want a better seat, no matter which kayak you get; after all, I got the Creature Comforts for my Pygmys. So don't let the seat tip the decision. (If you do get the Mill Creek, by all means assemble and varnish the slatted seat; it goes together easily, is charming, and serves as a good coversation piece).

As for width and leg comfort, again, I haven't spent a long enough day in my Mill Creek to assess that well. I'm not sure I'd let it be a factor, though. If necessary, you can block up the foot braces to narrow them. I think CLC could advise you. They have directions for doing that in their rudder kits (you need to block the foot braces out a few inches on the Mill Creek to gain clearance for the lines). In general, you'll find that building the kayak gives you confidence to modify and customize in all kinds of ways.

"About the building of the kayaks ... from what I have read, the Pygmy Boats
supposedly go together easier and the CLC boats need some shaving and sawing
to get the pieces to line up. Is this true? How difficult is this?"

I did find the "fit and finish" of the Pygmy pieces in both of my Pygmy kits to be more precise than my one CLC kit and, in general, I thought the Pygmys went together better. Both companies could benefit from having better construction manuals (they need someone to "edit" them with the perspective of a novice builder who doesn't already understand what they are trying to explain, much as third party companies have learned to do so well with software manuals). As for the shaving and sawing, yep, there's some on the CLC kits, as I described earlier. You can do it, though, if you have a generally patient nature and do-it-yourself instinct. I wouldn't let that drive the decision. Instead, try to pick the kayak you think you will like best and go into it knowing that if others with limited or no prior building experience have built it, so can you.

The hardest question is which kayak to build. For your uses, I see advantages to both styles, so I don't envy you the decision. But take comfort--if the experience of others on this forum is an indication, you may not be content to build just one (The Lays Potato Chip phenomenon of kayak building). It may just be a matter of time until you build one of each, and can take the one out that best suits your plans for the day!

Let us know, okay?