Did I screw up?

Firstly- I don't think there's a way for us to tell you which is the right size bike for you.  Your comfort would need to determine that.  Using an on-line calculator is one way to get there, but body measurements can easily be done incorrectly, especially if you're trying to do them on yourself.

But my bigger question would be the R1000 model? 
Isn't that bike from about 5 years ago?  Granted, if priced appropriately, it could be a good purchase. 

My concern would be that the LBS wanted a layaway/down payment for you to hold a bike that he's been sitting on trying to sell for 5 years. 

after getting my first "tri" bike this past summer.   i was absolutely amazed by how different they are from a road bike.  and trying to make a road bike fit like a tri-bike never really worked for me.   So my advice is to assess how many triathlons you plan on doing, and then figure out if it is worth it for you. There are many articles on the web regarding tri-bike vs. road bike.  just google it and read a few

Thanks for the input so far.   The bike is a 2006 model.  It is new comes with the standard Cannondale warranty.  It is better than half off the original price of the bike when it came out.  He didn't ask for a down payment, after I decided that it was worth it I gave him the money.  We got me set up on the bike and it was comfortable.  Im not sure if I was set up for racing or if it can be set up for racing.  The other bike shop guys said that might be hard to get set up in a aggresive position due to the size.  I initially was going to jump right into the tri bike, but decided to go with the road bike.  Mainly due to the price and the fact that I can do more with a road bike if for some reason I dont get hooked.  Its frustrating.  This is for my first triathlon ever and there is alot to learn especially about the bike. 

In that case, since you're probably talking about well under $1K
I think you've gotten a pretty good road bike for a good deal.  
Brand new, with a warranty and LBS support.  Seems like a good find.

Probably time to stop second guessing yourself, and just enjoy the heck out of your new ride.  Congrats on the purchase. 

Fit is all going to be dependent on your build and what is comfortable to you specifically once you're seated.
The R1000 is a mid geometry bike that should be good for both road/tri applications. I have one as well and used to ride it with clip on bars and a ffd seatpost to be more aggressive for aero. I think its a great "mulit purpose" bike and even though I've progressed on to a cervelo tri specific frame, the r1000 is still here as a backup.