As for the Enterprise
letters, the E-A appeared to be a unique ship in Starfleet history in being a deliberate replica of a previous vessel. The whole point of giving this ship to the man who saved Earth (again) was to give him a personal memento and trophy (and a ship that turned out to be a completely expendable lemon, perhaps not coincidentally). Bureaucrats couldn't allow for two ships to carry the same registry, of course, so NCC-1701-A was the next best thing... We might very well argue that the E-A was the first
UFP Starfleet ship with an -A suffix, at least, if not the only one.
The -B in the E-B might have been a pure publicity trick, just like having Kirk aboard for the launch. The Cold War had just ended - surely Starfleet needed all the good PR it could get in launching a massive new starship! Two ships would then create a pattern Starfleet would be disinterested in breaking.
For the Yamato
to be at -E when the Enterprise
is still a -D isn't a wonder, considering the big gap between the E-C and the E-D...