What do you mean by overheating, and how did you determine that was the problem? Stepper motors are designed to run at fairly high temperatures. The general rule of thumb (finger?) is that you should be able to hold your finger on the motor for at least 5 seconds, assuming you have normal sensation.
Those are likely Kysan 1124090
steppers. From the datasheet
they're class B insulation motors, rated at 130C. or 266F. While the case wouldn't be as hot as the motor windings at it's limit, that's still pretty toasty. You could fry an egg on them and still be within specifications.
As a practical matter you wouldn't run them that hot, from the potential burn hazard alone, but as you can see they can operate properly while very hot. The 5 sec rule will keep them in a reasonable temperature range, but if they're already there look elsewhere for your problem. Remember that by reducing the current you're also reducing the motor's power and your printer's speed and acceleration.
If the motors were actually overheating, the Rev F printrboards set the motor current in the firmware, and reflashing the firmware may have changed the firmware settings - that's one reason you want to save a copy of your settings (like in your printer notebook) after any changes. Did you know what it was before you reflashed?
And for completeness, 3 point probing is enough to determine a plane and is all you need if your print surface is flat (there's some argument that you will cancel out probing errors with more points, but they're fairly weak, since at best it'll be less than a step size's extra precision - and those step sizes aren't really all that accurate (think as much as 20% error)), and no amount of probing will compensate for a warped bed (unless you're using a (iirc) a Prusa Duet board and firmware). The Printrboard firmware only compensates for a flat surface, no warping. All that extra probing might look cool, but it really doesn't do anything useful. Better to spend that time making sure the head to bed distance is the same across the print surface with some measuring (the copier paper trick, or a dial gauge if you're more serious). It's commonly, incorrectly, called bed leveling. Autoleveling does better the closer you get to real non-auto "leveled". RJ's and my plywood bed pluses are within a few hundredths of a mm without probing required - as they (or at least the occasional moose) say probing is best left to aliens.