I may be wrong or incomplete but I know of a few things.
To my knowledge, the frames are all the same, and they are the same as those FXR frames produced from 1982-1994 as the Superglide II.
They all used stock Evo motors, dressed up with a lot of chrome. The FXR2 and 3 used black engines and the 4 used silver. Trim and paint aside, they were basically the same as the 1984-1994 Evo powered FXR. (The 1982-83 FXR's used Shovelhead engines).
The FXR frame was always a favorite of Harley riders and Harley engineers as well--known for great handling and lighter weight. I believe Eric Buell designed the frame (or was a participant) and they were patterned after the Harley racing XR frames. Light and stiff but made up of a lot more individual pieces of tubing, making them expensive for the factory to produce. Harley knew that people still wanted them, and they still had the frame assembly jigs around, and they knew Twin Cam engines wouldn't fit in the frame, and that Evo motors were on their way out also. It all added up to the last chance to make them.
I think this is the reason they were made for two years--along with the small production numbers of thise first two runs. Lot of demand--little supply by year. 450 of each color (900 of each model) isn't a lot of bikes--not even one per dealership.
Aside from the paint and trim (seats, mirrors, grips, bars, wheels, etc.), the FXR4 had dual disc brakes on the front, as opposed to single discs on the 2 and 3. The FXR2 had a 21" front wheel and the 3's and 4's used 18".