Recommend that you mount the studs before joining.  Putting the rails on the studs afterwards is easy enough.  Your plans should have the seat position marked so it is easy enough to do a test fit with the hull sitting in your yard.  Make sure that you consider both horizontal and vertical positioning and have the paddler where their prefered paddling shoes.  If the kayak has a tight fit/low deck, it is a good idea to do the fit test with the exact seat (height) and put the deck on to make sure the paddler's knees fit.  If the bulkheads are not already in, make sure that you know where they go so there is no interference when you go to install the footbrace rail.  I have two different brands of footbraces.  Both have rails about 15" with about 12" adjustment so you have some margin for error.  Lastly, CLC sells a vertical adjustment kit which can be used to move the footrest both vertically and horizontally if you make a mistake.

Here are the studs about to go into my wife's Frej.  Stud positions are marked in pencil.  

Absolutely put them in first. Here's how I did it on my WD12 and I got a perfect alignment. I used the rails to self align the installation.

To determine the positions , I sat with my back to a wall in more or less paddling position and made a note of where my feet ended up. Then, starting from the place where the front of the seat back would be, I measured forward the same distance and made that the center point  of the rails.

Since you have the deck, you know where the aft end of the cockpit opening is. That defines a hard limit for how far back the seat can possibly be. You have all the information you need to get the foot braces to where the normal adjustment range will let you set them perfectly. As Mark says, you've got plenty of margin for error.

Good luck,

Laszlo

   Just the info I need. Thanks, guys.