The pump that went out was my main return pump, which was a little giant 4, and the guy taking care of the tank rigged a rio 3100 as a return pump, while I was still gone.  When I returned, I attempted to replace the pump with one of the custom sea-life velocity T4 pump, but the first one I got leaked, so by the time I got a new one, I had a soaked carpet, and the acros were melted away.  THe problem has persisted for the past couple of weeks since I got back.  When I got back, the only thing that looked bad was my colony of Fiji Pom-Pom Xenia, and it's still trying to make a come back.  As for the calcium reactor, It was down for about 10 days total, and I haven't checked the calcium level yet, but that could quite possible be the problem.  The skimmer was also down for a very short time, but that was only for a couple of days.  The weirdest thing was that all the sps's showed exceptional growth while I was gone.  I just can't figure it out.  If theres anymore questions that can help my get to the bottom of this, please feel free to ask and I will respond as quickly as possible.  
Thanks again,
drew