Yes, tune the carbs last. Complete the entire 3000 mile tune up schedule and then deal with the carbs. Tuning the carbs to an engine that isn't otherwise tuned to run well is foolish, imo.
Also, you will never be able to "nail it". The carbs don't have accelerator pumps. When tuned correctly you can twist the throttle up to one half total travel to get quite spirited or reliable acceleration in any gear. Twist more than that and the engine will wheeze from lack of fuel, and likely die if the trans isn't in gear to keep the engine turning.
I would shop for replacement slides and needle, just to avoid headaches and doubt. If the slide bore was scratched by the damaged slide, then shop for replacement carbs. If he sanded the needles, what clip position did he use during reassembly? Have the pilot jets been verified clean and clear?
Check that all the head pipes are hot. These engines do struggle for RPM when the cylinders aren't all firing.
Report what's been done to induction and exhaust. Any change from stock will have some repercussions regarding carb tuning. And certainly book value carb settings no longer apply.
The stock bike would do the the standing quarter mile in just over 14 seconds, which is faster than most cars.
Cheers,