OK, here is the deal so far.....

The passenger side is the side that has the misaligned hole, but it's only the front hole. The rear is fine, and you can take the piece of wood it's bolted to when it comes and use it as template to mark it for drilling the hole into the hood hinge so it fits.

I have installed/uninstalled the hood a couple of times so far, having to take it back off to redrill the round holes into oval holes to allow the hood to be adjusted forward more. The hood sits back too far. I had to walk away from it for a bit, it was pissing me off I think the holes need to be opened up about 3/16 - 1/4 of an inch to get the right spacing. My passenger fender is also going to need to come in towards the hood about an 1/8th inch.

Is the cowl area supposed to be so curved? Compared to the wiper cover, you can tell it's got more curvature to it and will allow more under hood clearance as I can place my hand inbetween the cowl seal/weatherstripping and the hood when closed. This may change once it's in place, but I doubt by much.
All and all, it looks great and seems like it will great once everything is where it needs to be

2005 Ford F150 SuperCab FX4 1964 Chevrolet Impala SS 1998 CSVT: 354HP/328TQ @ 10 psi, now gone