Yes, when pedal is depressed about half way the booster push rod will cause M/C to bottom out. The pic shown, shows the adjustment bolt out about 3/16’s, needed torch to get it loose. Will put everything back together and try again tomorrow. Where there different types of brake boosters used for these M/C’s?

No offense intended, but it's all right there in the FSM.  The booster is adjusted to work with the MC.  You have to put the flange on the booster and adjust the rod to the proper distance.  

The booster looks pretty close to right. Something else is going on