Whats the best way to align the doors when putting the hinges back on? Do the brackets and spacers that go underneath of them go in certain spots? Or are they all the same size and thickness?

How do I straighten the door out?

 

You just do it trial and error. If the door latch is to low and hits when you shut it, you add one or more shim on the bottom. Keep doing it until the door shuts easily and strikes the latch at the same height as when it is latched.

 

Someone here will inevitably ask, "Why do you want to put the doors back on? Run doorless."

Not for everyone.
Start w/o spacers first then build up using the process 4.3L XJ stated.

 

When I took them off it had a spacer under each hinge bracket. I would assume that you need them all.

 

Talk to aircruiser he takes his doors off all the time..

 

my doors are on but not aligned correctly are there certain shims to use or should i just get some washers.

 

im guessing the reason is bc his jeep is broken down and has been parked on the street for a while haha.