I blew up 5 tip102's and 3 arduino's trying to figure out where I went wrong. The problem was that I did not have a delay before changing the rate of pwn to the transistor. The problem is fixed and 90ms was as low as I dared to go. Unless you want to remove the package of a transistor very quickly I would not recommend using the code on github. I will update it in the next couple of days as it now seems to be working.