It would indeed seem the pad stopped working because you updated your softmod. I would try using the d2x v8 cIOS. There is a guide here on the forum for installing d2x (I believe you can find it in the other guides & tutorials section). The game will probably need a certain base IOS to work properly, but I wouldn't now which, so you'll just need to try some. USB Loader GX (others might as well, I don't know, I use GX) allow you to choose any IOS to load a game, so you could just install all the cIOS with different base IOS and see which works.