I went to a firearm dealer this weekend hoping to purchase a Para Ord LDA 45 ACP. I did not get enough info  because they were so busy writing up that dealer records of sale. Anyway, what fascinated me was the thought that if I get rejected by the DOJ, I get to pay a restockintg fee.
Exactly, how is the vetting process done?
I know for a fact that there is 10 day waiting period and you need to have gun certificate or something. Is the DOJ the Federal level or is it the CA DOJ when you are being vetted?
What are the grounds for getting rejected to own a handgun, other than the ususal suspects, you know, have a criminal record etc...

you not passing the saftey test is a red flag

Quoted: What are the grounds for getting rejected to own a handgun, other than the ususal suspects, you know, have a criminal record etc...

That's it.  This DoJ FAQ should answr most of your questions about the process.

You will need to get a Handgun Safety Certificate, basically a license to buy a handgun in California.  The study guide for the HSC is mostly lifted verbatim from NRA materials (without attribution, natch) and so is a pretty good primer on handgun safety and handling.  Your dealer should sell the study guides for 50 cents or a dollar, and he can give you the test and issue you the HSC when you go in to DROS the weapon (if you fail the HSC test, I'm not sure you should be permitted to walk around outside unattended, let alone own a handgun).

While you are picking up the study guide, also buy a copy of John Machtinger's How to Own a Gun and Stay Out of Jail in California.