Just a few thoughts...diagnosis at a distance is not easy:
Some obvious things you probably already did: make sure nothing on the inside of the hood itself, or along the firewall seam (like the three flat bumpers), or on either side of the engine compartment could prevent closing...check the hood latch to look for trouble...make sure nothing on the valve cover or in the engine compartment is unusually high (there have been cases of incorrect engine mounts resultng in a push-up dent in the middle of the hood)...maybe look at the two front hood hinges to see if anything might be preventing them from closing...eyeball the hood spring especially the loose end to make sure its not jamming against a relay or emission box.
Silly section: I'v had the hood safety strap stick out through the hood-fender seam...did not prevent the hood from closing...but looked very stupid.
To make sure the rubber bumper is not the culprit, maybe unscrew and remove the bumper and the threaded shaft entirely.
Eyeball the hood to see if it's warped or bent.
Richard M, NYC