Unfortunately, when you went over your boss's head, you firmly attached a target to your own back. As long as you are his subordinate, you are probably "hosed" as it were. Documenting all your work and your interactions with your boss is the only way you have of protecting yourself for the time being. However, if your boss is "well respected" and not liable to go anywhere in the near future, your hope to "outlast" him is probably a pipe dream. Talking to someone in the Human Resources department(I'm assuming there is one where you work) could buy you some time in your current position, but you might be better served to see if there isn't a position you could transfer to where you would have a different superior.
I've been in this position myself more than once, and sometimes no matter how hard you try or how well you document your value to your employer, it may just be a "no win" situation. Once I found myself in the situation where "someone's head has to roll" and I ended up being the fall guy due to absolutely no fault of my own. My only saving grace was that it was openly known that I had done such a great job, I was able to find a position with a competing company who's management I had worked for previously. Think about what your other options are now, before you are put in a position of having to make a change involuntarily.
BEST OF LUCK!