Welcome to the forum!! I'd be wondering if it just isn't a normal CJ braking system - you have manual brakes so it's not unheard of to have to press pretty dang hard to come to a complete stop.
To rule it out, you'll probably have to take a closer look at your brakes - everything from the pads to the rotor to the calipers. If all of that looks to be in good order, next step is to bleed the brakes, starting from those furthest from the MC (passenger rear) to those closest (drivers front) to make sure there aren't any air bubbles in the lines. Obviously make sure there's enough brake fluid in the MC. After that I'd worry about your master cylinder, unless there's obvious signs of leaking around the firewall mount.