Hi Hypa,
Both my wife and I have done some research into starting a 135 certificate and we have both worked closely with the Reno FSDO in the past through various past jobs.
The FAA really wants you to start on your own certificate so that you can become intimately familiar with it. The last FAA guy I talked to equated it to getting your Private Pilot's License. You have to go through the training as opposed to just buying your license to learn all the nuances of the project. It sounds like you are doing just that.
If you need some help, feel free to PM me.