Hi John - I feel your pain, the same thing happened to me when I removed the hood to repair spot welds between the top and bottom surfaces (..covered elsewhere in the Forum).
Its a pantograph hinge which means as the hood front arcs downwards towards the hood catch then the rear of the hood tucks down at the last moment to meet the scuttle height. If the rear of the hood sits above the scuttle when the front of the hood is closed on the latch then that's the issue I had and I suspect its the same for you. Its because the hood hinges haven't rotated far enough to do the final tuck down part of the motion. This happens if a) the hinge pins are worn and/or b) of the hinge has rotated slightly clockwise (when viewed from the side of the car) in the body holes and if I recall the hinge springs tend to drive this to happen. If the hood fitted OK before you removed it and now it doesn't then its probably (b).
I fixed it by propping up the hood with a stick (I always do this anyway as I?m afraid the hood hinges were a bit of a weak point in the Mark II design) and loosening all the body bolts on each hinge (note you'll need to remove the side trim panel in each footwell to get to some of the bolts/nuts) and rotating each hinge counter-clockwise as far as it will go and then tightening up the bolts/nuts while still applying the rotational force. That will hopefully fix the height issue at the scuttle so that the hood now aligns. To get the gap width to be uniform you may need to loosen the two bolts between the hinge and the hood support skin (this would have been solved by the 1/8" aligning hole you've seen mentioned). Be very careful as the hood is very heavy (as you know!) and perhaps better done as a two man job to make sure the paint doesn't get damaged. Slightly adjust the back and forth position of the hood on the hinge as necessary and retighten the bolts ..its a bit of a trial and error process without the guide holes but its doable.
The above worked for me (and one my own!) and was all done with the hood in place, good luck.
Last edited by Mark Norris; 05-02-2024 at 07:19 AM.
Mark Norris
C56G3186
1963 Aston Martin DB4 Series V Vantage
1951 C-type Jaguar (alloy replica)
1934 Lagonda M45 Tourer