do you have the manual for the game??? you can download it from IPDB.

not sure about the LEDs being lit all the time.
did someone try to unsuccessfully mod the game to add the extra flashers per the original design?

now about the flippers
if you look at the switch matrix table you'll see there are 2 switches dedicated to the end of stroke for the left and right main flippers.
switch 15 and 63 both on row 7.
a simple switch test in the diagnostics mode will tell you if the game is seeing those switches.
these switches close when the flipper reaches the end of it's travel.
they are completely separate from the 50V flipper circuitry but tell the MPU when the flippers are activated for things like the high scores and the "missiles" at the beginning of the game.

Todd