You will need to leave term C security, and get a shuttle over to E. It takes about 5 mins on the shuttle, or the walk is about 15 minutes but shouldn't be taken by the uninitiated. That connection is very doable, and there is elite/C/F security at E which should shorten the time needed--if your incoming is in any way late though, I don't like your chances at all.

If it looks like you'll be late before boarding in SFO, I would as for a possible reroute, either on the nonstop, or through JFK/IAD/ORD/PHL/CLT etc. THere should be many ways to get you to MUC that day, but you need to be proactive if things start to look bad.