Thanks. Yeah, I already figured out the wrenches and got the nut loose with the booster installed. What I was looking for was a measurement technique for the booster rod / MC adjustment. Luckily I was able to get a local Honda dealer to loan me the tool so now I don't have to worry about it.
I first set identical lengths for the booster rod and pedal clevis using the old booster for reference, but the new booster output shaft still protruded farther so I have to adjust anyway. The service manual also says to apply vacuum during adjustment. I did not notice it made any difference with or w/o vacuum.