Good Brakes are not that easy to come by especially when an uneducated prior owner or mechanic does the install.
When all the proper components are installed correctly the light weight Jeep should stop on a dime.
First off the system takes about 19-21 inches of vacuum for the booster to work properly. Dual chamber boosters will work better if your system is either down in vacuum or you live at a higher altitude.
Proper bore sizing of the complete hydraulic system is also necessary. That means the the bore and the stroke in the master has to be matched correctly to the drum wheel cylinders and or Disc brake calipers in respect to total fluid volume & pressure that is needed.......
Also a disc brake master needs a larger fluid chamber as compared to a drum brake setup. Proportioning valves and brake residual valves also have to be the proper size for each system. Most proper master's and or proportioning valves may have the proper residual valves already in place. Is there some variance there? Absolutely ............but if your system sizing is near the edge and you add a larger tire ( IE; more rolling resistance & weight) or are down on vacuum or a host of other deficiency's the system becomes unbalanced.
Last but not least is the need to have the proper ratio's at the brake pedal to the master cylinder........meaning the force applied by your foot and the ratio needed to apply that force to the Master Cylinder push rod even in a Power Boosted system has to be correct.
Be it incorrect sourcing of parts , sizing or a different pedal setup will all give you problems.
In both of your cases you need to do some homework to establish what you already have......once known then the problem can be fixed.
I would be suspect of the proportioning valve. If replacing this does not help I would go with a manual MC on a booster, smaller cylinder, softer pedal, more advantage. you will need to fab a plug to fill the hole in the end of the cylinder that the brake rod would go in.
