First, as far as Williams single player "Add a Ball" games go, it is normal on the early '70's series games for the the Tilt light to illuminate briefly when the last ball drains just prior to the Game Over light turning on. Without a schematic, I'm not sure but I'd guess a momentary contact switch on the score motor (on a cam with only one tip) is either dirty or out of adjustment/barely making contact. I have a Spanish Eyes schematic but my game room is in the process of being rearranged and games are taken apart so I can't get to the schematic to offer further help at this time.
As for your other problem, we have to isolate is the problem with the 5000 scoring which is tied to three wagons and three lanterns or since Klondike is an add-a ball style game, is the special also set to award an extra ball? If so, whenever a ball is added, the knocker is supposed to energize and make the noise. We have all seen many knocker solenoids burnt to a crisp, usually related to the replay unit being messed with or a stuck coin switch etc. Look at your knocker solenoid on the side of the main cabinet. If burnt, disconnect it and all should be fine. Replace the coil when you can.
If that's not the case, double check the "play adjustment" Jones plug. Make sure it is correctly plugged in. Try changing the setting if it was correctly installed and see if the game behaves differently.
Is it only the three kickout holes that cause the blown fuse and not the "Scores reel value" rollovers? if so, the proble lies in the "Eject relay" circuit but I can't understand why say having three mining pans would be different versus other combinations. I'm guessing that a fuse also blows when a Scores Reel Value rollover is hit with either 5000 point combination.
Look at the "5000" Relay; are any contact blades bent and hitting a blade they shouldn't? or look for solder splashes or wires off from the solder tabs making contact where they shouldn't.
Also look for the same thing on the "Rollover" relay since some circuitry is shared between these two relays.
Bruce