Hi David
Welcome to the world of Alfa Evolution, I suspect you might have been better off just trying to fit the new fender as a skin panel, but no matter now, you're committed now & your plan of fitting it 1/4" at a time is the right way to go - I would suggest you made some sort of jig to hold the headlight aperture at the same height as the LHS, you will also need to jig the suspension points to make sure that the fender goes on straight & level as your new piece includes the suspension mounting points. About this time you need to refit the bonnet to make sure that you get the aperture right - obviously front to back & also left & right gaps as well as left & right heights to ensure that the bonnet sides fit. Don’t try to fiddle with the bonnet, use it as a template to fit the fender to the car.
I'd suggest that you cut the vertical leg (in picture 3 above) off your original fender & then worked out where to cut & marry the 2 pieces together to get the best fit - I suspect this might be just below the radiator mounting & chassis rail. It's an easy bit to cut & shut to get the right shape.
At this point, don't worry about the transmission tunnel fit, that is completely secondary as no one sees this point, they will all see the bonnet / hood fit so get that right as well as the fit to the base of the windscreen.
The transmission tunnel portion can be shaped to fit - read beaten into place, you might even choose to cut away the firewall portion of your replacement fender & refit your original ??
Either way, suspension points aside (these MUST be right), the "fit" on the top is most critical & you need to make sure that you fit the bonnet & also the windscreen aperture. If the bonnet aperture on the new fender is too short, you will have to let-in a strip, if the headlight pod is 2" too far back, you might have to let-in a strip, or just accept that it is a hand built car & no two were ever the same, especially if you plan to race the car & not show it.
Don't weld ANYTHING until the suspension points are right.
You are not alone, I have to replace the entire nose, (skin panels) on my Dad's Spider - good panel & POS panel in hand thanks to GTD
When all else fails, GTD will keep you on the straight & narrow…
Post more pictures of your suffering
Ciao
Greig