I have had lots of TF. I can't exactly remember all the bolts. All I can say is 1/8 is not much to get. If you can see a place on the fender that would allow movement if you elongated the hole by 1/8. Do it. Don't drill it out bigger, elongate it/them. Also take a look at the other door, it's fit, how it clears when opening, it's fender....and see if you get any ideas. Sometimes the grinder will get it done (1/16 on one piece, 1/16 on another) but not on a painted truck. Take a rest and sit in a chair near truck and think awhile. Drink something with alcohol in it. It's 102 and humid right now, be careful.
Shimming will help if there is a place. You will have to live with fairly large gaps on these trucks. The only way to get show gaps is adjust/fix/modify everything before paint. Factory gaps have large variances.
The specified gap all around is .16 +/-.09. All alignment is done without strikers installed. You can see that big gaps were in spec all around the truck. The max gap allowed above is .25 !!!!!!!!!!!!!! They could ship a truck with 1/4 gaps in those days. The minimum gap could be just a bit more than 1/16 !!!!! Just get the door to fit and forget about the gaps it may create elsewhere. After driving it a few months, the concern will go away.
ALSO: "but its leading edge sits behind and too close to the fender's trailing edge." ....when you say "behind", do you really mean sits inward, toward inside of cab? or what?
Remember this PM I sent you?
Specification says: "door surface at front shall not be inside of fender surface but may be .05 outside for door to clear fender." (For Reference: 1/16 is .062)
You can see by the quote from the manual, that "behind" is NOT allowed.
Another ALSO: Please restate the exact problem that is happening. Be specific. The door actually fits but what? It won't open without hitting fender, won't close with out hitting. It touches while closed? Does it hit in one little spot or several? Remember it has to be proud of fender like the spec says. You can go more than the .05 if you have to. No big deal. The .05 is NOT a gap measurement it is a surface to surface measurement. The good news is you say the door fits great with good gaps, you are there and don't know it!!! Adjust door outward or fender inward or both... until it clears when swinging and go from there.
HAPPY 4TH.