If it brakes OK under light to medium stops yet not on hard stops, I'd suspect some air in the system, try bleeding all lines before anything else.
Luck and enjoy the Runner.
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2001 Limited 4WD - 346+K - SunfireRed\Thunder Cloud; - 265/75/16 Michelin A/T2s - Fat Pat's 1.5" BL - StopTech ANGLED rotors - In series 699 trans cooler, New Yota1 transmission, All new OEM suspension front to rear.