Several ideas here, but I don't know what all else you have changed out so I'll start kinda from scratch.
I gather that you obtained new disc conversion parts from Jeff at the shop along with a "new" disc brake master cylinder.
The drum brake vacuum booster is a single diaphragm (what we call the pancake model) and is barely adequate for the oem drum brakes. The oem disc brake booster is the dual diaphragm unit (about twice as thick in the body area). The pancake booster will work...but does not provide enuff boost/over-ride to really clamp the new calipers on the front without a very strong push from yore laig!
The drum brake system used only a "combination" valve which is used to operate the brake failure warning light system, that is all it does.
The disc brake system used a "combination/proportioning " valve which proportionally reduces line pressure to the rear brakes when the front brakes are applied. So either that part or a workaround is mandatory for a disc/drum combo brake system like you now have. The Scout II service manual explains all this stuff in detail and shows all the variations I'm describing.
If you do not currently have a functional proportioning valve, then the workaround for that is to plumb the front disc brake system direct off the rear reservoir of the disc brake mc using a union in the line if needed.
Then install a manually-adjustable proportioning valve in the line to the rear brakes only! Such a valve is readily obtainable, ihon has 'em on the shelf. Then play with the setting of that valve to obtain correct braking performance and lock it down, you will not change that setting again.
You will not have any method of illuminating the "brake warning light" by doing the workaround, but who needs nannystate shit like that? I don't need nhsta or cpsc telling me my brakes left the scene!
If the pushrod between the booster and the mc piston is burred, then take it out and "polish". That is pretty common and tells me someone used visegrips or channelock pliers on it to adjust.
Rig a vacuum gauge on the intake manifold and once the engine is warmed up, note the reading. It must be steady (not wavering/wiggling) and needs to be a minimum of 16"hg at your base elevation in chico. Up at paradise on the hill it will be about 2"hg less due to increased elevation!
Then while watching the vacuum gauge, pump the brakes and note the needle movement. It will "glitch" once and return to steady, that is normal. If it's holding steady vacuum when the vacuum booster operates, and the vacuum level remains a minimum of 16"hg, then ya don't have a vacuum leak. Also replace that check valve and grommet that is plugged into the front of the booster, those are about $3.00 and are a "maintenance" item.
If ya can't make 16"hg vacuum, then ya got an engine tuning/performance issue to contend with!