The 87-89 YJ comes with a 15/16” bore Master cylinder because the calipers are a different design and the booster is slightly smaller. A smaller bore master cylinder actually BOOSTS brake performance, just at the caveat of longer pedal travel.
with 35’s, there is no getting around the factory brake deficiencies. The true solution is a big brake kit and vanco/black magic brakes are pretty much the only companies selling anything worth a damn. You can swap masters or boosters but there is no real way to improve the shitty wheel brakes without getting rid of them fully.