Figuring a very rough estimate of an average of 2" per fret for a 6-string fretboard (which is not completely accurate but in the ballpark), 36 frets would be 72" or 6 feet. You'll need more than that to account for overhang, waste, practice, etc.
(Are you going to be able to use that many frets?)
The function of the truss rod is to reinforce and adjust the neck, so its length is selected based on the neck length. Of course, the neck length will vary partially based on the scale length, but also on other factors such as the location of the body/neck joint.