'02 Civic Si... six speed?

I just bought my son an '02 Si for Christmas. It's his dream car. He doesn't know yet... He's not getting it until Christmas morning.
I bought the car from a wholesaler that advertises on Autotrader.com. When I went to look at the car I could tell that it had been hit in the front. Someone replaced both front fenders with ones that have vents on the side. I figure that's a modification that he'll really like! There were other signs that it had been in an accident as well. But since it drove very well, looked really clean, and was bargain priced at $5995, I bought the car. The only thing I could find wrong with the car is that is seems like the sync may be going out because it makes a slight grinding noise when you shift into 6th gear. That's right... SIXTH GEAR! I came home and started reading all the reviews for the car and they were all 'glowing' just as I had expected. But it occured to me that they all mentioned a 5-speed transmission. Thinking it may have been an option, I did somo more research. Nope... not an option. Something isn't right. The motor is the 2.0, but I'm just not sure it's the right 2.0. How can I tell what the motor and transmission came out of?
Also, There is a couple of little things the car needs. It's missing the Si badge on the front grille, the V-TEC emblems on the side (since it has been repainted), and the motor cover that says v-tec. Any idea where is the best place to find these things, other than ebay? I've looked on ebay and can't find any of them except the side decals.

Thanks,

Maury