You have two totally separate issues.
Sounds like your mechanic does know much about deisels or Military Vehicles. That being said, spend time reading the Tech Manuals so you will be able to work on it yourself or teach your mechanic. I'm not tring to be cute.
Almost every diesel vehicle will have some sort of vacuum pump. Either mechnaical of electrical.
The brakes do use the powersteering pump to assist the hydraboost brakes. Spongy brakes usually indicate air in the system. Bleed them.
There is a mechnical vaccum pump for the transmission. It is located at the rear of the engine where a distributor would be located. It will create around 20in of vaccum.
This vaccum is used to help the transmission shift. The Tech manual covers how to check it.
Here is a quick breakdown of how it works:
Pump creates vacuum, since diesel engines don't.
vaccum supplied to Vacuum Valve on injector pump
throttle position works the valve
partial vacuum is supplied to the tranmission vacuum modulator
vacuum modulator helps tell the tranny when to shift.
Any air leak in the system will effect the shift pattern
Section 3-21 of the TM 9-2320-289-20 Tech Manual covers the checking/replacement of the transmission vacumm hose replacement.
I even posted an thread on how to adjust the shift pattern
http://www.steelsoldiers.com/cucv/50568-cucv-throttle-vacuum-valve-adjustment.html?highlight=vacuum
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Not just for you but everyone that owns or is thinking about owning a Military Vehicle:
The Government spent a lot of time and money creating the Tech Manuals. They are way better that any Haynes or Chilton manual can ever be.
Almost every possible issue is covered in them.