did you replace the trunion bearings? how about the spring clip that holds the pads apart in the caliper?did u make sure the rotor was fully seated on the hub body?did u put lock tite on the bolts that hold the rotor to the hub body?is the caliper operating correctly? do you have stock straight axle rotors or ifs/fj40 rotors with larger caliper?
all i could think of right now...
never heard of a bent spindle but its possible.