Had an hour to work on this today so I got the mud flaps mounted onto the rails.  Here's everything now that the paint has cured.
 
I double checked everything (measuring twice or three times then cut/drill).
 
I cut them using a pair of gasket shears and also a box cutter with a new blade.
 
 
I used each rail and hammered with a rubber mallet to "mark" where each hole needed to be drilled after aligning everything the way I wanted it to be.
 
I used my drill press with a 3/8" bit to drill the mounting holes in the mud guards.
 
Here is everything assembled ready to mount onto the Jeep.  I have the rails inserted into the forward tire mounts to show that everything fits.
 
I hope to get the rear mounts on tomorrow but that is going to be weather dependent.  Got to love the continuous freezing temperatures and the snow storms...that what I get for living in RI.
Just a note, the mud guards I choose are reinforced with fiberglass, which I didn't think would matter when I cut and drilled them.  I used my shop vac after each cut/drilling but my hands were a bit itchy afterward.  Good times.