getinfo will tell you how many blocks there are.  There should be 50105 50106 now.  If that is the number you see, you are good.

getpeerinfo tells you what versions the clients are at.  The majority should be 0.8.6.3.  If not, I believe restarting the program gets you different peers.

I think the danger of bad blocks being accepted is only there when most of the clients are 0.8.6.1, which is no longer the case.  However, the programmer could probably have prevented the issue by use of protocol version numbers (70002 -> 70003 in version.h) if I'm understanding the code correctly.  That would have made sure the new peers automatically reject the old peers messages.