the wind shield that fits a 2005 won't fit the 2006
It looks like the difference between the early 57105-02A and the new 57211-05 is new the new windshield uses a removable mount and the early piece, (obsolete) came with a mount that remained on the motorcycle when the windshield is removed. This change was made in the 2006 model year.
The 07 accessory catalog p26, #B covers the application of this windshield from 02 through 07. The catalog doesn’t exclude the SE models, but it doesn’t include them either. I’ll bet 50 cents that the 57211-05 will fit the 06 VRSCSE2, but I would still ask the local Dealer to confirm the application prior to pulling the trigger on this piece.
It is not uncommon to see lexan windshields trimmed to the appropriate height for custom applications. If I were considering a chop job on a windshield like this, I would try to find a method to space myself up out of the saddle the approximate amount that I needed to remove. This should give you some sense of how the windshield will perform at that relative height.
If you are thinking about trimming a lexan windshield, consider making a template of the top portion of the windshield so the original profile can be applied to the modified windshield.
djkak