Yeah, acne scars are a bitch. I've got a couple myself. You could
use a little concealer. If not in everyday life, at least on stage, where stage make-up on guys is acceptable. And actually concealer is slowly becoming a guy thing, according to several articles I've read, even if guys won't fess up to it.
Since you're dressing sharp, you're already halfway to being metrosexual.
As far as being read as a girl when you've got longer hair, it may be because you've got large eyes and lack a brow ridge, both of which are typically female. It also looks like you've got a heart-shaped face, which is also more typically feminine, especially with the soften jawline. (It's less common for guys because of their heavier jaws.)
Again, for stage make-up, you might consider a little contouring to strengthen the jawline and play up the cheekbones. By shading the cheeks, it might make your face look a little squarer -- if the cheeks look more hollow it may make the jawline look wider.