You never mentioned how the bike runs ?
1) Does it idle ok? if so, no problem with the slide not dropping down all the way.
Are the tapped holes for the idle screws drilled in the correct position in the boss on the side of the carb?
2) As the slides are moving up and down in unison, no problem with the carb sync.
3) How is the WOT performance?, if ok, I wouldn't worry about the slides going too high.
4) If you look at the dimples in the slide through the little windows, the dimples in my carb slides can move past the window.
5) How much free play in the throttle movement? It could be a problem with the cable, take a good look at the splitter arrangement.