I read somewhere that CVO bought 621 of the 900 99 FXR3's built by Harley, that's where my confusion starts.
You've got all kinds of things confused there. CVO is Custom Vehicle Operations. Just a fancy name for a very non-fancy manual production line (literally bikes on wood carts) that started the CVO production. It was a Harley operation. In a building disused at the York, PA plant. Started by the P&A side of the company rather than vehicle manufacturing.
1999 was the first year of the CVO bikes. They didn't even begin picking up the "Screamin' Eagle" nickname until 2000 with the SE Road Glides (triple red was the best that year; it's true). In 1999 it's also the case that the best of the two CVO models was the red FXR2. It's much cooler than the other production color (which we shall not name here) even though that other production got more chrome.
For a decent article take a look here:
https://www.cycleworld.com/back-when-harley-davidson-fxr-made-its-return-from-archivesBy the way, the "SuperGlue" was a special model released at the winter dealer show in 2001 as a 2001 1/2 model. It had Marelli Delphi ignition, reverse gear, and was the upsized version of both the narrow glide and wide glide affectionately called the "Fat Glide."
FXFASGSEG (FX Fat Ass SuperGlue Screamin Eagle Glide). Deadpool had one. It was cool.