Sorry I can't help with a solution but I may be able to help you come to terms with the situation if it's to do with the hood springs. (In the words of the well-known prayer, "Oh Lord help us to accept those things we cannot change, like out of alignment Chevy truck hoods.")
I had the same prob. Faithfully followed the instructions, got it perfectly aligned, tightened everything wrist-breakingly tight, checked the alignment again, confirmed it was perfect, bolted the support springs up, closed the hood--and gaps opened up at the cowl. Repeated this numerous times (presumably also repeating the same mistake, whatever it was), until I ran out of swear words, gave up, and removed the springs. Now I use a makeshift prop to hold the *#@*$#* hood open. Advantages of new arrangement: (1)good exercise lifting a heavy AD hood without sprung assistance (2) additional income from work-out classes for elderly neighbors with atrophied biceps (3) able to sleep again and (4) wife no longer refers to me as Mr Grumpy.
Good luck. If you discover The Secret Of Eternally Happy Hood Alignment please let us know.