Good luck, and remember, there are plenty of EXCELLENT schools out there besides Stanford, and your research group and the work you do in it is more important to your future than the name of your school.
On the other hand, your scores are probably quite below the average for Stanford applicants and your application might not even get read,... then again, it also might, so put a lot of heart in it! The year in Germany might be touchy, though. Schools like students with unique experiences, but they hate to see a whole year without physics. On the other hand, if you think a year of pure physics research and studying will improve your chances then by all means, go for it. But apply anyway; getting an application rejected will not hurt your future application chances at all. Just because you can't prove you're good enough one year doesn't mean you won't be able to prove it the next.
Also like the previous comment suggested, Stanford ain't the only fish in the sea and if you can't do the work you want to do there, it's better to up and do it somewhere else.