There are two things that I would have done very differently. The first is I would not have tried to clear the house myself, buddy or no buddy. I've had to clear a few structures by myself and it was by the grace of God that they were empty. Put me in any structure or building and send in two individuals to try and clear it and I can guarantee I'm going to kill at least one of them. Not very good odds in my book and hardly worth the price of material possessions. Let those who do this as a living conduct the searches themselves. That's what they are trained and paid for, IMHO.
The second thing I would have done differently is to call 911 as soon I some suspicion that someone had breaken into the house. Also, a call to report that you scared someone out of someone's house is not as a big of a priority as a report that someone had broken into the house and is probably still occupying it. So chances are their response time would have been a lot shorter had you called 911 before trying to clear the house yourself.