I'm not the expert at this by any stretch of the imagination. I haven't got mine sorted out yet, either, but I've fiddled with everything short of a die-grinder -- and that's next.
Pictures of my headache are below. (I feel your pain.)
That said, it looks to me like the up and down alignment on your passenger door is okay, but that the hinges themselves may be in too tight. I'm assuming that the door won't latch and that that's as far as it closes. That would be a filler candidate.
The driver's door looks like there's too much material under the top hinge and that it isn't close enough to the "A" pillar as a result.
If your car is like mine in that respect, the alignment of the fiberglass to the frame member is suspect, and you'll have to plane the areas under all four hinges to be parallel to that pillar on both sides of the car for the doors to align.
As Todd says, adding material on the passenger's side and subtracting it from the driver's side has to be done in relation to the framework the rest of the body is attached to. The allen-head bolts that pass through the hinge plates and into the car go through an unknown thickness of fiberglass and into metal box tubing at what should be right angles.
Are there diagrams in those notes to show whether the pillars are threaded deeply, or just a single cut with a tap and die? Mine are not backed up at all with nuts. They are simply threaded into the box tubing, and that isn't very thick at all.
Do you have a magnetic one-foot level? It would be most helpful if you did.