Oh I see...I misinterpreted .

First -find a way to hold the valve spring retainer in place ! You may be lucky enough to get some more clearance.

Here's what I would do- remove both nuts and visually inspect the threads. Clean the inside of the top nut. Swap it for another top nut and see if I am able to reach the desired gap(might get lucky here). Measure the valve dive before it hits the piston at TDC and compare with another cylinder(need dial indicator...).
Yes,altering the position of the top nut alters the overall length of the valve.
Exh.valves are sodium filled. I don't know the cavity looks like and if filing the tip is a good idea.

Do you find the nuts loosened on this valve every time you check?