Let me guess: Your truck had the weakass JN3 brakes, pancake brake booster, and small master cylinder.
Now you've upgraded the calipers to the JN5 spec, but you haven't installed the JN5 master cylinder or booster, or the thicker rotors. The bigger caliper pistons need more fluid, you need the bigger master cylinder to supply it...and the bigger booster to maintain power assist. Thicker rotors (and the hubs to match) would be nice but not essential. Apparently, there's enough piston still in the caliper when the pads are worn-out.
The JN3 master has a 1" main bore, and a 32 or 36mm Quick Take-Up bore. The JN5 master has a 1 1/8 main bore, and 40mm QTU bore.
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The booster is similarly huge compared to the "pancake" booster.
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I got all my brake parts from the Treasure Yard, from an extended-cab truck that would have come with JN5 or JB5 brakes.