how are the switches in test mode?
maybe you have some AC leakage across the circuits, giving you momentary open circuits?

set your DMM to AC, and check the critical DC circuits.

one other question, do the coils get hot with zero play after 10 minutes, or only with game play?

If the coils are fine without play, I would focus on binding.

ok, this is a Hail Mary,

(sometimes called A-B-A testing too)

put the suspect parts in your road show, and see if the problem follows the parts.

To others,
Please note the part I quoted where OP pulled boards from the Road Show.
Where are these LM339's that you think are suspect?

ok, since you swapped the fliptronics board, (thanks lloyd for confirming it has the LM339s'),
your swap rules out the LM339's, and the rest of that board.

Ok, I'm back at mechanical binding.

Care to swap one complete flipper assembly bewteen your two games?

If your heat issue follows the assembly, you know where to focus.

I'm still thinking binding.

just a reminder, both the coil stop, and the small bracket holding the coil, need to be seated squarely. (90 degrees to the axial line of the coil)

Don't let either bracket walk/turn while tighting down their fasteners.

ok, this should eliminate binding.

boards and LMM's were eliminated.

and the coils are cold when not played.

Now, I'm thinking your grounds are not good.
The problem needs to be with something that is common to the two flipper assemblies.

You should have zero voltage when measuring across your grounds.
Also, no AC ripple in the ground circuits (set DMM to ACC for this)

even more challenging, you need to measure across the grounds when the flippers are actuated.

oh, and just for the record, what version ROM are you running? (seeing if you have a prototype ROM)

this is possible,
Keep in mind, he recently swapped the assembly from the road show, to the Creach.

I think this possibility can be tested in the flipper test menu (if this game has that)

I know in later produced WPC games, there is a flipper test that actuates each of the circuits (high left, low left, high right, and low right)

building on the hertz question,
is your game a re-import?

might be worth verifying the voltage is set for US, and not for Japan.

I belive the Japan setting will run, but you get higher resultant voltages. If it is Japan, get it set right.