Ok, here goes....
I had to blunder through this myself and "discover" how this works and to be frank, it's a PITA!
I don't know any other way to do it for now, but the following is what I discerned about how the Fiero doors "adjust".
As I mentioned before, there are several axis that can be adjusted on the Fiero doors and both sides are the same.
After I stopped and thought about it, I realized that there are 7 basic axis of adjustment to each door.
It's only a matter of which hinges you loosen and what end of the hinge you loosen to make the required adjustments.
So, to avoid being any more pedantic about this, lets just get right to the different basic movement axis of the doors.
It's obvious that the door hinges can be moved at either the *door* side, by reaching inside the door structure and loosening the bolts inside. or the hinges can be moved by loosening the bolts at the cowl, (body structure), side.
One of the bolts on the lower hinge must be loosened from inside the car.
The 7 basic axis of Adjustment and what portion of the hinge must be loosened:
By loosening both the upper and lower hinges at the door side, the door can be "rotated" about an imaginary axis longitudinal to the car chassis
By loosening ONLY the bottom hinge on the door side and very slightly loosening the top hinge on the dor side, the door can be pivoted relative to the top hinge to move the bottom of the door in or out.
The inverse happens if you completely loosen the top hinge at the door side and slightly loosen the bottom hinge to pivot the top of the door in or out relative to the bottom hinge point

By loosening both the upper and lower hinges at the door side, the door may be moved horizontally inboard or outboard relative to the chassis structure:

By loosening either the top or the bottom hinge, or *both* hinges at the cowl side, the rear end of the door can be moved up or down in an arc relative to the hinges.
(This adjustment cures a lot of the "droopy door" conditions at the door handle and the latch.)

By loosening both the upper and lower hinges at the door side, the entire door may be adjusted directly up and down relative to the chassis:

By loosening both the upper and lower hinges at the cowl side, the entire door may be adjusted fore and aft realtive to the chassis:
(Note, tthis is the same for adjusting the angle of the door to cure the "droopy" condition)

NOTE: If hinge pins are worn, broken or holes in the hinges themselves are worn out of spec they should be repaired first before adjusting the doors
I have found it VERY helpful to get wooden shims, (wedges), like the type that are used to shim and align household interior door frames and use them to evenly shim the Fiero doors at the bottom between the sill and the door structure and work by trial and error, opening and closing the door until you get the door gap as even as possible all around the door and the door latches easily, swings open and closed without catching on anything and operates smoothly.
I also suggest working with the side glass installed in the door and in the *up* position.
To keep the glass from hanging up on the rubber seal and making moving the door around difficult, simply lube the rubber with a light coating of vegetable oil that you can wash off the rubber and glass later.
You want to continually check the postion of the glass against it's rubber seal and make certain that it seats into the proper location all around.
Once you think you have it correct, be certain to cycle the window up and down a couple of times to be certain that the glass re-seats into the rubber properly each time.
If it is necessary to make *extreme* adjustments to the door, you may need to lower the window glass, adjust the door and then adjust the window tracks to align the glass as required.
In order to easily reach the hinges on the cowl side, you will need to jack up the car and remove the front wheel and fender liner on each side.
To keep from inducing any amount of flex or twist in the chasis so that you get the doors aligned best, I strongly suggest that you place jackstands under the front crossmember and keep the car evenly supported while the front wheels are off. If you find that the angle of the car on the jackstands makes it difficult for you to work with the doors, then raise the rear of the car and use a 2nd set of jackstands to level the chassis.
(I told you this was a PITA

)
Actually, none of this is terribly difficult work, (except reaching inside those doors to get at the hinge bolts if you have big hands), It's really just tedious and requires a bit of trial and error..check and recheck, until you get the best fit.
It's also worth mentioning again that the Fiero is a 1980s GM car and you will NEVER get the door and panel fit quality of more modern cars, plus the flexible nature of the Fiero panels makes it even more difficult, that said though, it is possible to get the doors aligned evenly and nicely with some effort.
I know some of this is probably as clear as mud and I didn't explain it well, but I hope it helps, and as always I'm happy to explain further and help any way I can...
[This message has been edited by randye (edited 10-24-2011).]