Question #1: Your wallet is showing that you spent .0005 bitcoins on a transaction. This was paid to the bitcoin miners. The .0003 never really left your wallet. It may have gotten shifted around to other addresses in your wallet internally but all the coins are still there. Your wallet is parsing that transaction you linked in the blockchain as Ins - Outs, that is (8.7634 + 0.0003) - 8.7642 = -.0005

As for the size limit, it was really that your transaction was too small that probably triggered your client to request a transaction fee. The other reason would be the actual physical size in KB or a transaction being large, but your transaction shouldn't have been large in that way because it wasn't very complex.

Question #2: No, you cannot specify which addresses to transfer out of. I'm not even sure there are any clients that allow you to do this, but certainly not in the default client.

Question #3: I believe this was already answered, but I would add that 10 minutes is the goal the system tries to do. The Difficulty is adjusted upwards or downwards every so often to try to make it take 10 minutes. This is to keep the creation of new BTC on pace as designed.