Because this just started happening after the mounts were changed, let's assume that the misalignment is in the vertical direction.
And, because you only changed the rear mounts (that's true, right?) the height of the B pillar rose in relation to the A pillar.
The door is hung on the A pillar and is securely fastened to it (by the hinge bolts).
The latching process takes place at the other end of the door. There are two basic components involved; the striker and the lock. The striker is firmly held in place on the front face of the B pillar. The main body of the lock is inside the door and is secured in place by screws that pass through the rear face of the door. There is a latching mechanism that is exposed at a cut out in the rear face of the door skin.
When the door is shut the striker "strikes" the latch. The latch can rotate and when the striker hits it, it snaps closed around the striker. The door is "latched" closed and will stay that way until the lock is released by either the exterior button or the pull handle on the inside of the door panel.
I am sure you can see where this is going. In order to re-align the latch with the striker, the back end of the door will need to be raised.
The hinges on the front end have bolts that point in two different directions. One set goes front to back and the other set goes from outside to inside. It is the second set - the ones that secure the hinge to the A pillar - that you will be working with. Be advised: the top bolt on the upper hinge is screwed into the hinge from inside the cab. There is an opening way up on the inside wall - almost up near the speaker - that allows access to the bolt head. The heads of all the bolts are the same (9/16" IIRC)
Loosen all six bolts, but only enough that you are just able to move the hinges by lifting up and pushing down on the rear end of the door. Next, spray some lubricant down between the pillar and the face of the hinge and re-tighten the bolts. Make them just tight enough that you can still move the hinge in relation to the pillar but the hinge will stay where you leave it when you let go.
When you have the hinges tightened like this, go to the back end of the door and shut it. You may have to temporarily loosen the striker. Move the door up/down and front/back until you have the gaps like this:
Gap between door and rocker panel is 6 mm plus or minus 2 mm (0.24 inch plus or minus 0.09).
Gap between door and roof panel is 5 mm plus or minus 2 mm (0.19 inch plus or minus 0.09).
Gap between door and the door pillar is 5 mm plus or minus 2 mm (0.19 inch plus or minus 0.09).
Gap between door and windshield pillar should be 2 mm plus or minus 1.5 mm (0.08 inch plus or minus0.06)
Those are the factory specified gaps, but you might have to deviate from those measurements a bit to get the striker and latch to line up:
Close the door slowly, and watch the engagement of the striker/latch. As the latch nears the striker, lift the door up or down as necessary to get the latch to accept the striker and snap shut when the striker hits the pawl.
Go to the hinges and snug the bolts up - but don't do the final torque yet. Test your alignment by swinging the door shut normally. Don't try to help it. If it can't engage itself loosen the bolts and continue until you find the "sweet spot".
The last step is to adjust the striker in and out so that when the door is flung shut normally, the latch closes around the striker and the trailing edge of the door is flush with the outer face of the B pillar.
This is not an exact science especially because (if) you only changed the rear mounts and the truck is getting old.
