Dr. Livesey is The Doctor HimselfWell, if he was Merlin, this can't be too far a stretch.
Long John Silver's pirates are secretly Patriots agents traveled back in timethey sent back in time to Captain flint's treasure, and the Patriots ordered them to kill John Silver if he helped out Captain Smollet
Alternatley, Long John Silver's pirates are secretly collaborated with the The East India Trading Co.
Long John Silver eventually invested his share of the treasure to open a seafood restaurantObviously, it became huge later on. You may have even eaten there.
Long John Silver is Jim Hawkins's biological father.Hawkins is the only child of a man and his wife who live in a remote tavern some distance from even the nearest village. The father is sickly and dies early in the story, just after Billy Bones's first stroke. It is likely that he was not virile enough to father more children despite all the dull winter evenings he and Mrs Hawkins must have had to pass, and what is more likely than that he was not virile enough to father Jim either? Meanwhile, thirteen or fourteen years previously, John Silver was not a crippled ex-pirate of fifty, but a well-off plausible rascal of thirty-odd, and could perfectly well have caught the eye of a neglected wife in a remote tavern. Hawkins senior, of course, would have kept quiet about any doubts about Jim's parentage, lest he become a laughing-stock. This explains well why Silver liked Jim from the start and was willing to defy the whole pirate crew rather than let Jim be put to death, and why he trusted Jim not to run away with the doctor, and why he backed Jim to side with him in the final confrontation with the pirates.