It took my previous employer about one year to get his initial part 135 certificate. From what I've heard, you fill out pages and pages and pages about how you plan to comply with each little section of part 135, then send it to the FAA. 2 months later, they send it back with all the parts they don't like highlighted for you to fix. Repeat this process once or twice, and eventually you get approval.
I don't have personal experience doing this, this is just what I've heard. You might want to take a trip to the FSDO and talk to them about it.