[CSRoad]

Is it a 49 State or a California spec bike? There are hose differences as in number and where they all go.
49 state is easy just fuel lines, bowl vents and the fat hoses are diaphragm vents. Cali has the same, although not plumbed that way stock and extra vacuum ports which need plugging.

Anyway my thoughts.

As a starting point I'd suggest a FactoryPro kit: CRB-H39-3.0-TH

Honda, vt750, Shadow, H39 Series

Really, after wading though the process on my own, that's my advice. It is expensive, but will save a lot of messing around. Give them a phone call and see what they suggest.
It gets you a set of adjustable jet needles that are a more suitable fuel delivery profile for the modifications, something that most other jet kits are missing and just give you shim washers for the stock needle, that IMO is the big thing.
I would go with 42 pilots (slow) and 140 rear main and 138 front main (Keihin sizes), the mains are probably a bit rich. but the spark plugs will tell you.
If you go with that jet kit, it comes with 42 pilots and an assortment of mains.

For tuning they have good advice and really the only logical way to approach it, as everything is affected by the main jet choice.

CV Carb Tuning Procedures

Click on the Low Speed link and follow along.

You will likely have lost bottom end and created a mid-range hole with the open exhaust which you will have to finesse the tuning to minimize.
Open exhaust and intake don't really net much in the way of power at best, due to the nature of the cam timing and limited rpm range.
More in and more out, does not = more power if it can't swallow it.

Another thought, kind random, the left rear fake fins will fit the right front cylinder if you cut a square out for the exhaust port and make things look smoother with a full set of fins.
They often disappear from the wrecker/recyclers, but can be found with some looking and since you are painting them a color, finish won't matter.

 

[CSRoad]

These VD series carbs are more or less sidedraft CV carbs.
The California bikes will show a "C" on the end of the model in the parts listing like VT750DCA AC as opposed to VT750DCA A for 49 state version.

California bikes have addition vacuum ports for the vacuum valves for evap and canister purge.
Regular 49 state bikes just vent the gas tank to air and the float bowls to a plastic tee that has a hose that just hangs down below the carbs.
The fat tubes for venting the diaphragms on my bike I just have the elbows pointing downward to avoid ram air effects. Honda has the secondary filter box and the large tubes to avoid turbulence, they actually don't flow a lot of air but should see ambient pressure for correct operation.

Edited: because of the desk cat.

As for 48 pilots that is way too rich and will lead to crappy fuel economy. It will probably run and respond though.
Some "carb tuners" resort to huge pilots, crank the mixture screw in and then shim the hell out of the stock needle in an attempt to mask the poor transition from the low speed circuit (about 1/4 throttle), when a more reasonable pilot jet size and a thinner jet needle is needed. The pilot circuit will bleed fuel thoughout the operating range of the carb, but is in no way as efficient for fuel atomization as delivering fuel to the main venturi with a correctly sized main jet and needle.

Two more cents. (-:

 

[CSRoad]

The ones that matter are the bowl vents, the diaphragm vents and the fuel lines, the rest can be plugged. (-:
Refer to the picture: It is of a typical 49 state setup I had handy, the corresponding stuff on yours should be similar.
The ports with tubes each side of the "sync" screw are the bowl vents. On the outside of the carb bodies from that are the plastic elbows which vent the diaphragms.
The fuel inlets are where you would expect, usually with a T fitting and the hoses armored with springs.

On that type of pod filter make sure there is not a concentric "wall" on the carb end that blocks holes in the intake horn casting, if that happens trying to tune it can get miserable fast.

 

[CSRoad]

Yeah once you get it running you can pull the caps off and if they suck they were just a vacuum source and put the caps back on.