connecting to your phone through SSH is more than well documented already around these parts. And you have to jailbreak in order to do that, and this thread is mostly asking for how to do it sans jailbreak.
OP, what you could do is hack through the back up of your phone, find the plist that records the order of your apps, then delete the mentions of the stock app. Then restore your phone from the back up.
Have you tried this and does it work?