The board bottom is near-flat?
The dummy way is to lay it in the chassis and mark the holes with a pencil. Pencil must be perpendicular!
To be more accurate, drill one hole, run a bolt through (still flat to the chassis) and check the opposite corner hole. If OK, drill that and screw it. Now you can drill the other holes through the holes in the board, using it as a guide-plate. (If very fussy, drill 1/32" smaller to avoid wearing the board-holes, then enlarge after you remove the board.)
Painting the screw-tip "should" work, except they probably aren't quite square or centered. If long, they come down well off the proper place. Also the blob of paint is likely to hit more on one side or the other, making an off-center blot. This can work but may need several tries and corrections.
Do not feel bad. I ordered two bolt-on resistors, then two more. I measured one resistor carefully, marked for all 8 holes, drilled pretty close. The first resistor, I knew I'd slipped and I had to rat-tail file a bit. The next one would not fit, though the hole was dang near perfect. Finally slapping myself into sense, I measured all four resistors. The second batch were a good millimeter off from the first! Between my slips and my idiocy (not checking b4 drilling) it was a long session with the file.