Still not right, FFS.

[zed1015]

s-l1600.jpg So the ringed parts I blocked. Middle one is used for petcock vacuum. Is this correct?

The "ringed" vents MUST be left open to atmosphere.
The other on #3 carb is vac line to the fuel tap and must be capped if not in use for a vaccum tap.
Put your needle clip position and main jet back to stock .
The rebore and exhaust should need no jetting changes.
Open airbox would require air corrector jets and up a size on the mains.

[zed1015]

Going to sit down tonight and read up on Air Connectors.

You only need air correctors if running open carbs, pods, stacks or an airbox that has been cut or modified and offers virtually no restriction.
They cure the off idle bogging / hesitation and need no other carb changes except a small increase of the main jet.
In some cases such as the Yamaha XS1100 the main jet is actually reduced in size from stock.
In the case of the GS750 your stock main should be 102.5 and increased to 112.5 with corrector jets and no stock airbox.
Your current spec with airbox should need no jetting or needle clip position changes from stock and your 115 main is too big which with lose you top end power..
You should put all carb settings and jetting back to stock before going any further and uncap the carb vents.
The carbs overflow pipes in the float bowls do double as vents to a degree but at high speed their small bore can offer a restriction leading to fuel starvation .