I have recently acquired a 1998 Cherokee from my uncle which is in excellent condition and stock, however when driving it, I realized that the brakes weren't working as well as they should and I almost got in an accident on the highway. My father, who has previously owned 2 Cherokees XJ told me that it's probably the master cylinder and he often had to change it, however pumped the brake pedal while my engine was off and the pedal didn't go down.
After digging around on the forums, I found that many people recommend just installing a 99-'04 WJ master cylinder with it's dual diaphragm power brake booster or to install 99 Durango V8's master cylinder with a 99 XJ Cherokee's dual diaphragm brake booster. I have also seen people just saying to flush out the fluid and after replacing it the problem would be solved.
I really don't know what I should do, should I upgrade the master cylinder with the WJ's or the Durango's, or should I just change the brake fluid and keep the car 100% stock?

 

Your year already has a dual diaphragm booster. Installing a larger master cylinder will only make your braking worse.

Flush the fluid and adjust the rear drum brakes. If not sufficient, replace pads with semi-metallic at minimum, preferably performance/towing pads. NEVER use "lifetime warranty" pads; they don't work for crap, thus they last forever...