To have the extensive knowledge of earth and it's affect on a Kryptonian body then some Kryptonian scientists/explorers were there before.
I think it would be interesting if a few hundred years ago (or a few thousand) Kryptonian explorers set out to discover other habitable worlds. On each world they setup outpost to work from in remote locations so as not to interfere with native populations. The scientists were surprised when they landed on earth and the effects of the yellow sun. After years of exploring all the various off planet expeditions were recalled but the outposts remained intact and cloaked from detection. It's remained sealed for several thousand years.
Essentially the fortress is one of these outposts.
As one of Kryptons top scientist and scholar Jor-el is familiar with these outposts and places a key of sorts in Clark's ship that will unseal the fortress. It also has updated information on all things Kryptonian, so once Clark places it into the fortress everything is download and it updates the databanks so they included everything including his ships journey to earth and the planets final moments broadcast from Jor-el to the ship.
Also the superman suit is essentially an exploration type outfit Kryptonians used while on earth. They found that as they began testing the limits of their newfound abilities only clothing that was close to their skin remained intact. They developed the body suits as a sort of second skin and it inherited their invulnerability.
Also as far as motivation for someone like Brainaic, i don't think he was Kryptonian in nature but sought out the planets vast information, as it was one of the most technologically advanced civilizations ever known.
He once sought to absorb it's knowledge and destroy it as he'd done countless other world's only to discover this shining light in the universe was already destroyed. He's tried to find any trace of the Kryptonian outpost but b/c of the cloaking technology he can't locate them. He's sent out countless probes in search of anything Kryptonian. Eventually one probe lands on earth and finds Clark's ship, (Clark is a teenager at this point) and tries to remove the key (which will both lead it to the fortress and unlock its secrets). Clark has an altercation with the robot and destroys it, but recovers the key and begins his journey to discover his heritage. the robot is recovered by Lex Luthor, reverse engineered and eventually reactivated, it broadcasts its location to Brainiac's ship in space, thus leading Braininac to earth.
