The first time Sherlock Holmes saw John Watson he knew that this was it. It wasn't love at sight, but rather a quiet acceptance that this man would be the person he'd spend the rest of his life with. Sherlock was a genius, and used his mind to draw logical conclusions and gather useful information but what no one knew and what he'd deny to the day he died was that a part of what made him so brilliant was that he knew things. Most of the times it was small titbits of information, details that at first glance held no meaning but in the end was invaluable to the bigger picture. However once in a while the things revealed to him was life changing and enormous, with lasting consequences and the future relationship between him and John Watson was of that nature.
Sherlock realized that if he had been a creature of less mind and more emotion he should have felt confused, apprehensive, and most likely a little bit scared considering his lack of experience in the matter of the heart and body, as he had never before felt anything of sexual or romantic nature towards another human being. However Sherlock was a man driven by logic and not emotion and therefore did was any intelligent man would do; he absorbed the new knowledge into his mind and heart and felt his world shift according to this. Priorities changed places, plans were amended to include John, his apartment was mentally being rearranged to accommodate the new part of the household, and he let the emotions that would be tied to the man settle in his heart. In the end Sherlock remained the same, but with an added truth in his soul: John Watson's was his and that was that.
The first time John Watson met Sherlock Holmes his gut instinct instantly told him to run. Run fast and hard without looking back and never ever stop. Because Sherlock Holmes was a dangerous man, a man that would take what he wanted and wouldn't even hesitate or ask for permission. However John Watson mind knew that the things his instincts were screaming were absurd and therefore did what any self respecting man would do and ignored those instincts, shoved them deep into his mind buried in the dark recesses of his mind. It wasn't until later he remembered those instincts and rued his stupidity. Because while he didn't regret his choice to stay and face Sherlock it would have been nice to have been a little more prepared.