Just to follow up for anyone who may come across this thread in the future with a similar problem...
I chose to save the development cart and implement it because with the 1.5 upgrade I opted to redesign the entire website layout and use different mods and clean up every inch of code that had been mangled in my previous 1.3.9 cart.
Disclaimer: The steps I took worked flawlessly (so far) however I would never recommend going against DrByte's wisdom. I have a decent working knowledge of all parts involved with the zencart system making it a little easier.
1. I took 60 screen shots of every setting screen in my v1.5 cart. I use
http://www.screenshot-utility.com for quick screen shots (auto save).
2. I created a backup of both my live 1.3.9 cart and my v1.5 including database backups. I also made a back up of the CEON URI table that had all of my redirects already setup.
3. I sent my live 1.3.9 site to Mx mode so no one could order or create an account.
4. Deleted the v1.5 database and imported the backup of the most recent 1.3.9 database I had.
5. Uploaded the zc_install directory to the v1.5 directory and followed the database upgrade steps.
6. Then after accessing my admin area all of the mods had pretty much disappeared except for a couple that don't use sql for storing settings.
7. I went through the documentation for each module I had previously installed on the v1.5 site. For some modules I just had to run the SQL install script that came with the module. For a couple I re uploaded the non-core edit files and refreshed the admin page and ran their on page installs.
8. For me in particular I then imported the CEON URI table so i wouldn't have to go through that hassle again. You could just follow the documentation included with CEON to manually add all of your URIs again.
9. I spent about 2 hours going through the v1.5 site and admin area verifying everything was running smoothly and changing settings to match the screen shots I had previously taken.
10. I then followed the standard upgrade instructions to bring my v1.5 site online and archive my 1.3.9 site.
I may have missed something here. This is just for reference.