1) You'll need access to all 10 bolts on each door's hinges, which means the fender will have to be at LEAST loose enough to pull out a few inches. Totally gone is better, but then you have more work realigning the fender after you get the door done. But you have to align it even if you just swing it out, so it's probably worth getting it totally out of the way if this is your first attempt. I've replaced my door hinges & aligned them enough times that it's not that much trouble for me to work around the fender.
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2) There's no point in even attempting this if your hinges or strike bolt bushings are worn/damaged, or if the doors or body are bent, so check all of them beforehand. If you can lift the open door & hear a clunk from the hinge pins, find some good ones or get some hinge repair kits. The strike bushings can be replaced, but if you don't have the later strike with the crash bracket that wraps around it, it's worth swapping, and they're easy to find in the junkyards in good condition.
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3) The door can be aligned, but it may not seal to the body if the foam rubber seal has collapsed. It's expensive to replace, but EASY to repair by simply filling with a foam caulk backer, available at most hardware stores in the weatherstrip section. The seal's steel core should also be re-crimped to grip the body lip tightly, cleaned, and the face should be lubricated with silicone spray &/or dry teflon lube.
4) I think the hinge bolts are all 13mm, and I know the strike bolt is a T50 (like the seat belt bolts). A cordless impact is invaluable. I also recommend some padded prybars to lift/slide the door without chipping the paint. As you can see in the 1st pic under #1, you'll need a few extensions & a ratchet to break & set the bolts. All of the nut plates in the body are loose (for adjustments), but captive (they shouldn't fall if the fastener is removed), but anything can happen. If one falls, just remove the interior trim panel & retrieve it. To reinstall the strike bolt nut plate, you'll need to remove the bedside panel & peel the butyl (tar) pad away. The plate itself will be behind the shoulder reel on the floor, or on the bag of wadding crammed in down there.
(This photo is blurry - I'll try to remember to get a good one later)
1) Ford describes the process differently, but assuming the hinges are reasonably close, I've always started with the strike bolt. With the door fully closed, note any misalignment up-&-down between the body lines on the door & the lines on the body.
Adjust the strike bolt as needed, checking CAREFULLY for perfect alignment. If the hinges are FAR off, skip to step 2, then come back to 1, and do 2 again. When closing the door, be careful not to crack the strike bolt's plastic sleeve bushing, but the door must be FULLY closed (on the 2nd catch). Fore-&-aft alignment (gap spacing) isn't critical at this point, but do make sure the rear edge of the door is flush with the body (in & out).
2) Once the strike bolt is set, loosen all the hinge bolts, then use a ~1/4" thick shim to level the door to the threshhold. A piece of heavy hardboard ~12x24" is ideal. A loaded door is fairly heavy, so be prepared for it to shift when the last bolt is loosened. Do NOT slam the door shut since this might damage the strike bolt's plastic sleeve bushing. Lift it carefully onto the strike bolt & close the latch FULLY. Using the shim, raise the door so the top edge is parallel to the rain gutter. Since the latch is holding the back on the strike bolt perfectly aligned (RIGHT?) with the body line, keeping the top edge parallel to the gutter will set the whole door's vertical position & alignment. I typically lift the hinges as high & forward as possible on the cowl before tightening one bolt, and then make minor adjustments. This keeps the heavy lifting & prying to a minimum. Concentrate on the cowl-side hinge bolts first, since the door-side hinge bolts are only to adjust the seal pressure. Center the door horizontally between the A- & B-pillars, IGNORING the gap along the fender at this point; you're only concerned with the fit along the A-pillar. The fender will be aligned to the door later. Use the door-side hinge bolts to align the door's LOWER front seal pressure (between the hinges) so it touches, but doesn't cut the foam seal. Ignore the window frame for now. Open & close the door several times to make sure it's perfectly aligned immediately BEFORE the latch engages the strike bolt sleeve.
3) Next, check the rear edge's alignment with the quarter panel. If the strike bolt is already set, this should be OK, but a warped door will be tight above the bolt & loose below, or vice versa. Don't be afraid to gently twist the entire door skin using a towel in the jamb & pressure from outside. When the entire bottom of the door fits right, check the window frame. It's easier to twist, so don't go too far. Remember that too much seal pressure in one place will open a gap in another. A piece of dry paper (like a dollar) should be difficult to slide all the way around after being closed in the door.
4) The final adjustment is to the latch height. With the outside button held in, and working VERY slowly with your eyes on level with the body line, observe the door's movement JUST as you push it closed & the latch comes in contact with the strike bolt. If the door rises EVEN SLIGHTLY, slide the top hinge forward on the cowl to lift the back edge of the door. If the door drops, move the hinge rearward. Ideally, the "V" of the latch opening in the door shouldn't touch the strike bolt's plastic sleeve bushing at all until the door is fully closed. This minimizes wear on the bushing and gives the doors a "showroom" sound, which is very noticeable once you've heard it.
1) Lube the latches, hinges, & strike sleeves with a good flowable grease - not a penetrating oil (PB Blaster, Liquid Wrench). WD-40 is the cheapest stuff I'd use, but it's more of a wax than a grease. White lithium spray grease is OK, but the best would be a flowable synthetic grease with PTFE (teflon), like Wynn's Viscotene or Winzer Polylube 250. Apply a dry teflon &/or silicone spray lube to the body seal, and glass runs (in the window frame, the vent window, AND down inside the door).
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2) After moving the door, the fender will have to be realigned to the door, and (if it was completely removed) to the grille. You shouldn't have to align the hood to the fender unless it was wrong before, but that's just a matter of twisting the corner pegs & possibly raising/lowering the hood latch (2 bolts). Aligning the fender involves cardboard shims on the cowl horns near the hood hinges & probably some prying on the lower rear fender bolt (on the bottom) to adjust the gap along the door, but it's fairly straightforward. I'm not going into that in this thread, anyway.
2) The only other adjustment that might be needed is to the courtesy light switch. It only needs to be fully extended, and then closing the door will adjust it automatically. If the switch looks fairly clean (no corrosion), spray some penetrating oil on it & pull the black plunger out HARD to slide the brass tube out of the nut. If you think you're going to break it, remove the switch from the cowl & follow the procedure shown in this pic & the several following ones.