I'd start by undoing whatever you did.
If the 300 and 3 Bonus relay were only giving 200 and 2 Bonus it sounds like it was deactivating early:
Once the score motor starts turning the 11B switch (in red) should generate 6 pulses (in red) headed for the Bonus Unit step up solenoid. The 6 pulses need to get through a normally open switch on the 300 and 3 Bonus relay to get to the Bonus Unit step up. When it's working correctly the 300 and 3 Bonus relay should let go after 3 of the 6 pulses when the score motor 6B switch (in red) in its lock in circuit opens. That should block the last 3 of the 6 pulses.
If you hold down the 300 and 3 Bonus relay I'd expect you to get 6 pulses not the 2 you were seeing.