Bump, because I'm interested as well.

EM coils usually (not always) give indications of being bad, such as a dark brown burnt appearance, melted bobbin, cooked paper wrapping. I haven't done a Bowler yet but the principles are close in all EMs. Sounds like the motor is under load and can't turn or a short. Manually spin the motor with a wooden stick to ensure it is free.
Look close at all solder joints, sometimes the tabs cross one another and short.
Check that all mechanical linkage in back is free. Look for crossed wires or disconnected wires that could touch where they shouldn't.

When I first read, I was going to suggest checking the 10 pin coils under
the pin hood, but you stated that you disconnected that from under the
coffin. The Lock Relay is suppose to stay energized once a game is started
until the machine is turned off.
A Coil and Relay Coil will burn out before the fuse blows. You said that
all bottom board Coils/Relay Coils seem to be okay, but had you carefully
look at the coils in the Relay Bank? It could be others in the Bank, but if I
had to guess, I'd fist check the Start Relay Coil, and 2nd guess would be to
look at the Game Over Relay coil.
If any of those coils in the Bank are burnt, it should visibly be noticeable..

Yes, if a Relay Coil was burned out, it would stand out. I'm sure you checked for solder
splader, especially in the Bank. This can be tough. I've seen where a single steel wool
stran caused hamic..
So with the 4 head plugins unplugged, along with the pin unit's harness, (you sure it's
the pin unit unplugged and not the plug for the rollovers) (just making sure), it pops the 50V
breaker a couple of seconds after the machine is turned on..
Before anything else, if any of the relays in the Bank Relay is in the energized position,
had you tried manually resetting the bank and then turning on the machine? Probably won't
make a difference, but slight chance that it could..

I think your assumption is very likely.
I haven't done this often, but after I no longer have anymore fingernails left to scratch my head,
I've put a bolt in the fuse holder and looked where it first start smoking. This is highly "NOT"
recommended, but best, with all the plugins unplugged like you have, and with the machine itself
unplugged but the toggle switch on, you can have a Friend with the power cord plug in one hand,
and a plugged in extension cord in the other, and as soon as your Friend plugs in the machine, he
consentrates primarily on the Relay Bank, and you the rest of the bottom board, and as soon as
a puff of smoke is seen, the machine gets unplugged, with your Friend always ready in an instint
to unplug it. I've done this alone with no problems and your machine won't burn up, but I suggest
having a Friend along so any further wire damage doesn't take place. Even if it's contacts that's not
suppose to be touching, that's where it will fist start burning..
This might be the only time I've suggested this without being on sight..
But before you do that, if the coin mech is still attached, had you checked the Coin Reject Coil
at the lower right front inside the coffin? If the coin mech has been takin' out, maybe checking any
Coin Mechs loose wires in that area. If some are (taped) together, you might want to separate them
and then turn on the machine and see what happens..

Glad that worked out!