[xcelr8]

1) In terms of the fitment, what is the best method of making sure everything lines up in the end, doors, fenders and cowl ? Is a test fit with fenders installed the best way. Doors are still on the car.
Place your bottom pan in and secure with a couple sheetmetal screws, then top pan. Put on entire front end (fenders, hood, doors etc) and adjust from there. You really want the car at least loose assembled so you can get the gaps right.

2) Also is it best to weld the upper and lower sections together first and then weld in the entire assembly.
No. Weld the pans in separately. Bottom pan to the car first then top pan to that (after the above step has been done and your reference points noted)

3) Finally, what is the optimal hole size to use for the several hundred plug welds in the lip of the vents.
I used a Harbor Freight spot hole cutter to make the holes in the new cowl. Same one I used to remove the factory spot welds.

You can see my cowl job in the link below.

 

[xcelr8]

Thanks! Yeah, nearly 10yrs of work but enjoyed every mile this first summer driving it

I bought a gallon of Duplicolor Bed Liner from Advance Auto and used that on the lower cowl pan as well as the underside of the upper pan. Complete bottom of the car and my interior floor pans have it as well.

If you plan on using that export brace I would include it in your mock up. If your shock towers move in or out with or without the brace installed, that means your fender bold holes in the upper aprons are moving as well which also determines where you fenders will sit. Now there's some adjustability left/right/fwd/back via the fender bolts, but more you can assemble up front the better.