Let me tell you a story with 3rd party HD's and Apple repair. My friend got his logic board fixed for free because he had a 3rd party HD. They must have fixed it first then asked about the hard drive. When he got the call about the repair bill making it to $900 he told them to send it back and he would put the old HD back in. When he got it back it was fixed.
A similar deal happened to me!
The Apple repair center called wanting $900 to replace the hard drive before they would fix the logic board. They also made a couple of excuses as to why the upgraded hd might be the problem. They were misleading me, so I ranted a bit because the Genius knew the HD was an upgrade, but made the repair offer anyway. They sent it back, I put the old hd in, sent it back to Apple. It came back repaired for no charge and with a new battery!
It's like a new computer, except for some squiggly lines on the screen. Apple said it was from pressing down on the laptop while closed. Anyone else have something like this?