I don't know if the short bed 2wd has a two piece driveshaft? If it does, the center carrier bearing rubber mount may be causing the vibration in the lower gears until the driveshaft rpm increases enough to even out the pulses caused by the u-joint angle. You may also have loose/broken motor/transmission mount/mounts.
Although you didn't exceed the GCWR for your truck it looks like the trailer has 5 lug wheels which should mean 3500lb. axles by two equals 7000lbs gross trailer weight. With 6000+lbs. of rock plus the trailer (2000lbs?) just a little over. Looks like a well balanced load, and leaving lots of extra stopping room is the key.