I don't think you will see any change in shifting with the spacer mod.
I noticed an improvement in shifting when I switched to 20w-50 Mobile 1 MC oil. The 10w-40 isn't great for smooth shifting.
Changing the handlebars on the Vee is a must do. I went with ROX risers and Pro Taper ATV mid height 7/8" bars with a crossbar, love the setup, and it got rid of the vibes in the bars.
SS lines and good pads help on the brakes. If you want more front brakes there's an easy 4 piston conversion available, you just have to pick up a set of used calipers.
I went 2+ teeth on the rear sprocket and think it's perfect gearing. I did the upgrade to 530 chain when I rechained. Use the front sprocket from the VL1000 which comes stock with 530. I have a JT rear sprocket.
Getting a good map in the power commander and a good TB sync will work wonders for smoothness and power, but don't expect good mpg. I average ~37 mpg.
My wife & I have ridden 2 up on both the Vee and FJR, my wife likes the Vee better, it has very good passenger seating.
The factory center stand is nice to have.
13 MG Stelvio NTX
09 Duc Sport Classic 1000
09 Kawi KLR650
00 Suzi DRZ400-S