Scott, Mike Kubarth who I believe is the foremost authority on all matters related to 40 Fords posted this response to a similar question I had:
Anyone that's restored a '40 Ford knows the trials and tribulations of installing and properly aligning the front sheetmetal.
We all know that the factory alignment was usually quite poor. It's true there is (was) little room for adjustment when these vehicles were new.
Please understand I remain in a constant learning process and am certain there are various ways of properly aligning the sheet metal. However, the way I'll describe has worked for me on numerous occasions with wonderful results.
I start the front sheet metal alignment only when I am completely satisfied with the door alignment. If you're restoring a convertible, it's a MUST that the top be completely installed (in the up position) and functioning as well.
Running boards are not on the vehicle at this time. It is FAR easier to install them later and adjust the rear fenders to the boards.
It is in my opinion, imperative that the hood be installed and aligned to the cowl prior to any fender(s) / grille work is installed. Take your time at this step. It is important that you have good hinges and springs. There should be no wear at any of the pivot points. If there is, the adjustments will be (more) difficult at best and the alignment will not last.
Be careful that the gap is even from side to side both along the top (between the hood and top of the cowl) and each hood side. Be certain the same amount of gap exists between the hood and the cowl. The height of the hood should be even with the cowl. Remember that a persons eye will be drawn naturally to the side of the vehicle and especially to the straightness of the trim and body line. It is imperative that these lines are straight! Bottom line -- the hood MUST BE CORRECTLY aligned. Take your time and get it RIGHT! Before moving on tighten all attaching points. There should be no need readjust the hood later.
Prior to installing the fenders I elongate and enlarge the four clearance holes that will be used to bolt the fender to the lower cowl.* Also at this time I enlarge the four holes in the front of the fender that the grille will later bolt through.*
The grille should be a complete assembly PRIOR to installation. This is important as there is no allowance for adjustment within the grille assembly. Originally the stainless strips at each side of the grille (Deluxe only) were stapled to the sheet metal louvers. Doing this makes the installation a bit neater and positively easier. On concourse vehicles be certain to use round wire staples. Flat staples were not used in 1940.
Now it's time to install the inner fender panel to the respective fender. Prior to this installation enlarge the clearance hole at the bottom (near center) of the inner fender panel.* This hole will be used later to bolt the inner fender to the frame directly next to the brake hose bracket. Be certain to enlarge the correct hole. Of the two holes in this area one will contain a grommet while the other is intended as a clearance hole for the fastener. There is a caged nut on the inner frame to accept this bolt/washer assembly. Bolt the inner panel to the fender at the top using the special flat carriage bolts. Tighten all securely. On concourse vehicles a thin webbing material is required between the fender and inner panel.
Now's the fun part!
WITH HELP, install a fender / inner panel assembly. Loosely install the nut/bolt assembly through the 'Y' brace to the inner panel. Install (snug -- not tight) the four bolt / washer assemblies at the lower bottom of the fender to the caged nuts within the cowl. Now install the other fender.
Again, WITH HELP, using the eight nut / bolt / washer assemblies install the grille assembly between the two fenders. Again, snug -- not tight.
Now's the (not) fun part!
There is no easy way to do the remaining aligning. However, patience is an absolute must! Do not be surprised if this takes two, even three evenings. I tend to 'walk away' when I become frustrated.
Slowly and methodically push / pull / tug on the fenders and grille assembly until you are somewhat satisfied with the alignment. Keep a careful eye at the horizontal gap between the hood and the grille (top) as well as the vertical alignment of the hood to grille.
Tighten the bolts at the grille / fenders just a bit more at this time. Recheck all the gaps. If you remain satisfied move on to the four bolts at the lower fender edge / cowl. Tighten these a bit more too. Do the other fender.
Continue to recheck all the gaps after tightening each area.**
Tighten the bolt / nut assemblies at the 'Y' brace. Again, check all of the gaps to be certain nothing has moved.
If you remain satisfied with the entire alignment it's time to tighten all fasteners securely. If you are not satisfied you should be able to push / pull at the fenders as thus far the attachment points are only snug. Remember, "snug -- not tight"? This allows the sheet metal to be moved a bit into place and hold it there prior to firmly securing the fasteners.
If this tightening causes the fenders to pull in too much it is practical to install a thin washer between the fender panel(s) and brace. On reproduction panels I've found it necessary to enlarge this hole (inner panel) just a bit.
Lastly, install the lower radiator air deflector. It may be necessary to enlarge a hole or two in this pan. Not to worry -- all are covered by the proper fasteners.
* I enlarge the holes to 1/2" and elongate approximately 1/8" on either side of each hole. The elongation should follow the curve of the fender. Remember that all these holes will be completely covered by the correct body washers.
**If any gap should change after a specific area has been secured you know with certainty which area caused the effect. You may need to elongate a hole or two in that area a bit more. There should be NO binding at any attachment points.
