I'm not sure what your issue is, you installed a 'breaking system' (SIC) and it broke your braking system.
I just looked in the 9300 manual, it doesn't state explicitly to activate multiple times, but it does say a few times that system should not be used with engine running, not designed for non-power brakes, etc.
The 9700 manual does have a big box at the top of page 10 with a CAUTION to always deplete the vacuum before towing if you have to start the engine of the towed vehicle.
I have an older unit like yours, I guess I figured this out without the cautions, plus I always test multiple times to make sure everything is in position and it is working properly. All the manuals discuss the unit is designed to work with power brakes discharged, so I knew to depress pedal a few times, enough to bleed off vacuum before driving off.
I would imagine the brakes must have been near breaking before use of the braking system, a few hard applications of the brakes should not have done $1700 damage to your auto.