SO I yanked my doors off when it was beautiful the other day. Got pulled over 10mins later went home and put them on. Now it seems like my drivers side has a large gap at the top of the window. I dont get how you would go about aligning them seeing as how theres nothing slotted where the bolts go its all just straight forward holes...

 

Never done this on a toyota, but if they were alligned previous to being pulled off and then not alligned when you put 'em back on, I'd loosen them up and try moving them around a bit.

To answer your question - typically the adjustment is under the kick panel, where the hinge attaches to the body of the truck.

 

just a side question: did you get a ticket or just a warning?

 

I think you answered your own question, otherwise if they were just bolt holes then they would align up when you bolted them back on.

Haven't had any Toy doors off, but everyone I have seen has an adjustment in hinges to body and hinges to door area. If you didn't move the hinges to body, half your work is done. I am guessing you unbolted from door, which means possibly vertical up and down and facing door to opening, in and out. Even if you unbolted from body and left hinges on door, same principle. Will take some familiarizing yourself with the movement and adjusting a little at a time.