I have a 1989 IROC that I have swapped with an LS3 and Magnuson 2650, and now curious if anyone else here has done this and what is the best way to measure for hood clearance.

 

I've used modeling clay on the areas that are close. Place a clump or ball of it on the lower clearance spots on the top of the engine and slowly close the hood. If it's not close to closing you're gonna need to get creative or dish out cash for a new hood. If the clay compressed a bit and it fully closed you may need to clearance the areas compressing it. I used this method on my trans am hood.