It sounds like you're pretty convinced it's the wheat germ, but I'm  pretty doubtful that such a minor change in your diet could be the sole cause of your break outs. Acne and breakouts are influenced by a multitude of factors; diet is only one. Hormonal changes, stress levels, weather conditions, and all sorts of other factors in your life can (and DO!) lead to pimples and acne flare-ups. Although changes in diet can occasionally cause skin issues, usually it doesn't happen over night and happens when there has been a pretty radical modification... like if you were chowing down on a couple cups of wheat germ every day! In fact, wheat germ is often prescribed as a nutritional supplement for people who struggle with acne! Just google "acne and wheat germ" and see what pops up.

Pimples are a pain, but don't trouble yourself too much. If you haven't had big issues with acne up until now, they will probably clear up in no time. You know the drill... wash your face with good quality soap, avoid pore-clogging make-up, and moisturize!

Oh... and if you're still certain it's the wheat germ my first thought for a sub would be wheat bran or oat bran.