Had a 97 Fatboy with front rocker box issues. Finally figured it out. The lower rocker box had a small chrome bump on bottom side of corner. It was always difficult removing the front exhaust rock arm shaft when box was bolted to head. Put some sticky back sand paper on a flat inspection stone and sanded/lapped it back flat. Worked good after.
Probably a rare case but thought I'd throw it out there.
I loved that bike, but don't know if it was because it was really a great bike or because it was my first Harley. A little of both probably.
A version of your sanding method was my always my go-to for the too often slightly warped rocker boxes also. Good flat surface (machinist's table, counter top, something that works) and some sticky sandpaper then slowly work the surface until it's flat. I haven't told the FXR yet that it'll get sanded yet. However.....
After noticing the rear leak I looked everything over even more closely and with a really good light. Ever so slight leak on the back and a seep on the front. Both could run for a long time but they'll get some winter maintenance this year. Which led me too.....
Gawd we just can't leave stuff alone. So I was thinking (those words rarely lead to anything cheap)....
Don, I says to myself, if you've got the top off both heads anyway you might as well.....
Well, you know where that's ending up.....