Blown engine?

Some of you will know that my bike has been in the shop for over a month now. This is prime riding weather for me and its really killing me to be caged. On the tenth of last month, I changed the engine oil, transmission oil, and all the filters (both oil-1 and air-3). I had done this before so I figured I knew what I was doing. After the regular maintenance, my friend Ralph and I took it for a test ride. Between 1/4 and 1/2 mile it had a huge power loss. I turned in at the first side street and it died. I tried to restart with no luck. There were no indicator lights of any sort, so the theory was that perhaps I had sprayed the air filters with a little too much filter oil, causing air starvation. We quickly removed them and tried to restart with no luck. I had dinner & club reservations, and was going to propose to my girlfriend that night so we trailered it back to Ralphs. I came in a day later and changed out the plug thinking lack of air caused it to get too much fuel and flooded, fouling the plug. Changing did no good. Both of us were unsure what to do next, so we decided to take it to the shop. They closest one was Station Park Honda, but they apparantly can work on about any bike. I double checked with them and Yamahas are no problem. The mechanic told me "hopefully it will be something simple like the carburetor." which sort of worried me. My bike is fuel-injected and does not have a carb! I didn't hear from them for about a week, so I went in to see if everything was ok. That's when they told me it would be another two to two and a half weeks before they got to it. I was bummed, but resolved to get it fixed. I went in every week and they said "almost" and "just a couple ahead of you". Finally they got to it on a Friday, and called me with the news. "Your engine is blown and will need a rebuild costing $1000-$2000." I was shocked to find this out because nothing I have done would indicate the bike's engine was ready to go.