First, can you upload any other simple sketch to the Micro?
Second, you don't seem to have posted the code for the entire sketch that is causing problems. You must show us that if you are to get any useful help. If it is long (hopefully not) please add it as an attachment so it is easier to download.
My guess is that your enormously long interrupt routine is the problem. I always try to restrict my interrupt code to 3 or 4 lines.
...R