Trying to check/align sheetmetal gaps by eye can be frustrating.
A measuring standard comes in handy. I usually use a paint stirring stick/wood shimsstock, but spare change will do for a quick reference. (wrapping them with electrical tape would keep them together and protect the paint)
I checked the gap on a few vr4's, and they all fell into a fairly narrow range.
Two quarters shows the fender top to "a" pillar and top of the door nicely.
The front doors can be tricky, as the clearance varies depending on where you check it. The door has some extra clearance built into the middle section to prevent it from catching the fender when it's opened.
Just get it parallell with at least a two or three quarter gap, and you're good to go

Top of drivers door ( near front )

Top of drivers door (near rear )
Like most high mileage vr4's, the hinge pins on this car have worn a scosche, and this door has settled at the rear.
To adjust this gap, you will have to access the hinges where they bolt to the body.
Usually, you will have to adjust
both hinges to compensate for the wear/sagging.
Adjusting a door with severely worn hinges will not achieve very good results.
To check for hinge pin wear, open the door and lift it up at the rear. If it moves more than a little, replacing the hinges will probably be your best bet.
You can also get a good indication of the wear by closing the door gently against the latch. If the back of the door raises as it latches, it's time to look into the situation a little more closely.
The drivers door will show the highest amount of wear/sag, as it's the one that gets used the most. In the case of JNR's fender intereference, it's one of the first things to check.
First, check the hinges for wear, and the door for sagging by checking the clearances of the front door to the roof and rear door.
If everything is good there, check to see that the fender hasn't been pushed in at the rear. They are fairly flimsy, and can be distorted easily with a shot from a neighborhood kids football/basketball.
After you hunt them down and kill them, you can deflate their football, remove the inner fender liner, stuff it into the gap, and
slowly inflate it to pop the sheetmetal back into its original shape. "Bumping" the sheetmetal above and below the concave area
gently with the palm of your hand will help the metal relax and take the set you want.
Go easy, and take your time or you'll end up with an "outty"
Many times the best way to set the door/fender gaps is to start at the rear door. Get it perfect, than move to the front door, check the hinges, replace or adjust them, set the front door up, and then set the front fender gaps.
A good lubricant for general automotive use, this works
really well on door/hood/trunk hinges and latches. Use the straw in the nozzle, and wipe up any exccess to prevent attracting dirt and grit which will accellerate wear.
[public service announcement]
While you're in the area, take a moment to clean out the debris that collects at the bottom of the fender. It will trap moisture and lead to unnecessary corrosion.
[/psa]