Both "Man shot in head, but notices only five years later" and "Man shot in head, but only notices five years later" are grammatically correct. The meanings of the two sentences are different because of which word the adverb 'only' modifies. Only, as an adverb, should be placed nearest to the word that it modifies.
==> Notices only 5 years later seems to imply that the duration of time was only 5 years as opposed to being longer.
The placement of 'only' immediately prior to five years causes it to apply to the time frame, as you suggest. However, I don't think the intention was to imply that it was only five years as opposed to being longer. I think only is applied to the five years to underscore the fact that it actually took five years before being noticed. I think that was the author's intent.
==> I would say only notices, not notices only.
That's fine, but it would change the meaning of the sentence, causing only to apply to notices. That would mean that the only thing the man did was notice that he had been shot. It would mean that he didn't go to the doctor or engage in any other action. He only noticed. Again, while grammatically correct, I don't think that was the author's intent.
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