When the LB/Double Bonus relay trips the bonus count circuit driving the L/1000 point relay changes slightly:
Big Indian Double Bonus (resized).jpg
I'd start by checking the two switches in the red box.

/Mark

It sounds like your double bonus is subtracting too fast. It should slow down to count a double bonus. If you're sure the circuit in reply #6 is working properly have a look at the switch in the red box:
Big Indian Double Bonus 2 (resized).jpg
If that switch doesn't open the bonus will always subtract at full speed and not slow down for the double bonus.

If your Bonus Unit takes 5 steps at a time between pauses on the double bonus you need to figure out why. Here is the circuit again.
Big Indian Double Bonus 3 (resized).jpg
There are three different paths that can drive the Bonus Unit subtract solenoid. They all start with the Score Motor 1A switch on the right which generates 5 pulses per 1/3 turn of the Score Motor as shown in the Motor Sequence Chart. Only one of the three paths should be used at any given time.

The bottom path used only during reset goes through the SB2 switch and allows all 5 pulses to reach the subtract solenoid.

The middle path through the normally closed part of the make/break switch on the LB relay and a switch on the Q relay is used when a single bonus should be awarded. It also allows all 5 pulses from the 1A switch to reach the subtract solenoid.

The top path goes through the normally open part of the make/break switch on the LB relay and a switch on the Q relay and is used when a double bonus should be awarded. The Motor 2C and 3C switches allow only the 2nd and 5th pulses from the 1A switch to reach the subtract solenoid. The other three pulses are blocked.

The theory is that somehow all 5 pulses are getting to the subtract solenoid from the 1A switch when the double bonus is being counted and only the top path should be used. If that's the case the pulses are likely getting through one or the lower two paths. Either the SB2 or LB switches aren't opening correctly, or their solder tabs or wires are touching or there is some other kind of electrical path through them. It's also possible that the 2C or 3C switch is stuck closed or shorted which would allow all the pulses through. You'll have to inspect things carefully and experiment by blocking some switches to see if you can figure out how the extra pulses are getting through.

Nothing in the game happens faster than the 5 pulses per 1/3 Score Motor turn generated by the 1A or 4A motor switches (apart from maybe a playfield spinner).

The scoring circuit is shown above in reply #4. During a regular bonus count the Bonus Unit steps down at 5 steps per 1/3 turn and the L/1000 point relay keeps up by adding 5000 points per 1/3 motor turn through the upper path in the circuit in reply #4. The effect is 1000 points per Bonus Unit step.

During a double bonus there's no way for the L/1000 point relay to add 10,000 points per 1/3 motor turn so instead the counting has to slow down. The Bonus unit takes 2 steps per 1/3 turn instead of 5 and the L/1000 point relay fires 4 times instead of 5 effectively giving 2000 points for each Bonus Unit step.

In the circuit in reply #4 during the double bonus the Make/Break switch on the LB relay adds the normally closed motor 3C switch to the circuit. That switch allows the first 4 pulses from the 1A switch to get to the L/1000 point relay, but opens to block the last pulse from the 1A switch.