1. As written, once a legacy ability runs out of steps that's kinda it. Which is indeed rough for darkvision because you can get it up to some crazy numbers without trying that hard, so as a houserule for grades III and above I'd reduce the error range on Awareness and Perception checks made in Dim, Faint or No light by 1 per additional grade to a minimum of 0.
2. Yes, they can stack and cancel each other out: +2 Dex/+2 Any/-2 Any has the same reasonably hefty build cost as +4 Dex/-2 Any.
3. The -2 penalty for additional racial feats at 1st level can go anywhere you ant it to go, though ultimately your GC has the final say on how many you can pick up. The lowest a PC's stat is allowed to drop is 3, so if you start with a stat of 8 you're only going to be able to burn that stat for 2 (8->6, 6->4, then no more as you can't pay the 2 attributes points and drop to 2).
If you are munchkining like that, then the GC has pretty much every right to declare that the PC has no capacity for more than rudimentary independant thought (you might be a genius, but you don't have any sort of drive to enact that intelligence unless directed), and unthinkingly follows every order given to them by the rest of the party. And that would be on top of the potentially crippling hit that character would be taking to their Lifestyle and Legend, and the justifiable tendency of others to react to their presence with torches and pitchforks.