1) is a bug that's been noticed, steve has also put another sample game database in the release thread that can be successfully deleted , to use it just drag that stevefire.db into your game folder, overwriting the old one.
2) that's how aurora works, as the game drags on and more NPRs exist or your own empire expands calculation speeds slow down, having less NPRs always helps, or changing sensor update type,if you're using 7.0 (also listed as 6.5 on the initial game window) try changing to no updates in systems player has no presence in for a significant speed improvement. It will mean that NPRs will always be neutral to everyone untill you stumble into their systems.
3) scientists have always been random, you can use space master to add more officers untill you get some decent researchers, I usually do.