Not sure what happened with the couple of insta-posts before I even started trying to type, but whatever.

It is your boat.  Make it fit you.  If you can decide within an inch or two of where your but will land on the bottom of the boat with seat installed, use that as a reference.  Or note that the back of your back will be about 3 inches in front of the aft edge of the cockpit coaming.  Just figure out a good reference point.  Then sit on the rug in "kayak" position - knees bent to the extent that feels correct to you.  Get a measurement from your butt or back reference point to the balls of your feet.  Might as well get one from the floor up to the balls of your feet while you are at it, too.

Since you are short, unless you anticipate kids or even shorter people using the boat, I'd position the footpegs on the rails so that they only have a couple inches of additiona aft travel, with the remainder being forward travel adjustment.  Measure the distance from the back face of the footpeg to the aft hole of the adjustment rail.  Subtract that from your butt-to-ball of foot or back-to-ball of foot measurement.  Use that length to measure in the boat from your butt ar bacl referemce point in the boat up to where to drill the aft rail hole.  Judge the height of the hole based on your heel to ball of foot hight estimate.  Double check to make sure it all looks right and makes since, make some marks, drill holes and mount away.

Good luck!  That's the good part of building your own boat, you get to make it fit you, and you get to make your own mistakes.  Jut tonight I'm planning out how I'll make the floorboards in my Rhode Runner as a removable unit (not screwed down individual slats).  I'm not interested in having to unscrew floorboards when I drop something between the cracks into the bilge. or when it gets muddy down there.  Figuring out how to make the modification is half the fun.  And I haven't even started wiring the hull together yet.  I wake up thinging about these things all throughout the build.   

Hi Elb, 

with respect to your question, while you may adjust the foot rails fore/aft, their height should not change.

i have found that the design positions on these boats are usually pretty accurate for the range of folks who will likely ever be in these boats so unless you are really really short, you will probably be able to adjust the footpegs aft to fit you even if you put the rails in where CLC recommends.

bubbleheads point about measuring is never a bad one.  i just find that it can be a bit complicated to get an accurate measurement - and at the end of the day, you are trying to translate it into rail hole location. 

all that said, if you mess it up you can fill holes and redrill them if you mount the rails with thru hull hole (vs internal mounts that don't go through the hull.

h