I'm willing to go out on a limb here and say that there's probably NOTHING WRONG with your carburetors. Everyone seems to automatically point their fingers at Webers without realy looking at what has happened.
These guys changed the oil and adjusted the valves and then, all of a sudden, it starts to bog on shifts. No rough idle, supposedly no change in the carbs and now it bogs. And when you take it back, they magnanimously offer to pull your carbs and re-jet them to overcome the bogging. Really?? And would YOU be paying for this "upgrade"???? Pardon me while I drag my eyebrows down off the ceiling.....
Oh, and by the way - you can change Weber jets without removing the carbs from the engine - did they know that??
YES....take it to a much better (and different) shop. One that might not retard the spark just enough to cause it to bog on shifts. Maybe they had good intentions and checked the spark advance just for the hell of it, found it somewhere around 12-14 Degrees BTDC at idle, didn't understand that it has a centrifugal advance distributor that must be set at 30 degrees BTDC at 3,000 rpm, not at idle and set it back for you and THAT's what's causing your problem. Inadequate timing advance will cause it to bog between shifts.
The only other thing I can think of is messing with the stroke of the accelerator pumps on the carbs or checking the idle mixture screws (both easily messed with), but I would first check the igntion timing. If that's set correctly, then we can look elsewhere but I wouldn't mess with the carbs just yet.
I agree with Jim - go see Larry Jowdy.
gn