Car Registration Renewal from inoperable status?

okay, here is the "low down" on my situation.

by the way, take it easy on my as this was my first car and my dad just threw me in the pool on this one and told me to "do my homework" on this.

I live in Northern California, My 91' Acura Integra has been inoperable since 2010 and when the DMV sent me mail for renewal my dad said he checked inoperable and sent the the Letter back to them.They stopped asking me to renew the vehicle and recently my Uncle swapped the Engine out to make it run better than it did when I had it and after it broke down obviously.

I renewed my insurance for 2012/2013 and have not had the car smog checked yet.

I was wondering what steps I should take to have my car re-registered as operational.

I checked put in my license plate #, last 5 of my Vin and zip code, checked passanger vehicle and annual vehicle registration renewal on

www.cartagz.com and they said I owe the DMV. WTH???

As of 12-17-2012

DMV Fees: $621.00

Cartagz Service Fee: $29.00

Convenience Fee:$15.53

Total Due:$665.53