I recently traded my 2003 Deuce (88) for a 2011 CVO Street Glide (Wife fell in love and made me buy a new Harley). My brother has a '05 Deuce and my neighbor has a '06 Deuce. However, we truly loved our Deuce. In my humble opinion it is The Best all around scooter Harely has made. We've taken 2000 mile trips without complaint and your typical weekend runs were a blast. LOVED THE DEUCE!!
Both the '03 and '06 bikes have the older style cam chain tensioners.

The problems with this system have been mixed. Some riders have never had any problems while others had horrible failures. My brother changed to S & S 510 G gear driven cams at about 35,000 miles with no visible where. I changed mine to the S & S 510 G's at 32,000 with visible wear (scalloped pitting) to the cam shoes and one of the cam bearings was failing and starting to burn the shaft. My guess is that it would have failed at any moment.
I'm pretty sure that Harley corrected this issue in
'07.
If I were making the choice I would consider the mileage and overall finish on each as well as the price difference. If both were good then I'd probably go with the '03 CVO Deuce because it is a 100th Anniv CVO bike.
With either choice I would highly recommend a cam change right away just to keep a little piece of mind. I had mine installed by a local builder for right a $1000, tuned, Etc.. Harely dealers here in St. Louis wanted something like $2,300!!!!
Cam choice is a widely debated topic but I can only say good things for the S & S 510 G's. They are a mild cam and the all around ridability was great. It made a big difference in performance. Note! It was not a wild power house but I used the Strong to describe how it ran with these cams.
510 refers to the lift (.510). These cams are a bolt in style and are very easy to install. Mine was an 88 so I'm sure the S & S 510 G's would really wake up the 95" motor, not to mention completely eliminate the older style cam shoe issue. Then again you cam install some high compression pistons, port & polish the heads, and stick in some crazy lift cams for fun.
Good Luck with your choice. Keep us posted.