Cobalt327 offered up valuable information in his post #2. He may have gotten busy and can't come back to follow up right now. Here is the information from the Holley engineers about boost-referencing the carbs. He gave you a link, but I don't know if you saw it.
"QUESTION What is a Manifold Referenced Power Valve?
ANSWER Nothing will kill a blower or Nitrous engine quicker that a lean condition. You want plenty of fuel available for the engine to use .There is a thing you need to know about the power valves on a roots style blower engine. The power valve is installed to keep the engine from loading up and running rich at an idle. On a naturally-aspirated engine the engine vacuum at idle will hold the power valve closed. When you step on the gas the throttle plates open and the engine vacuum drops as you accelerate. When the vacuum drops below the rating of the power valve, it snaps open and richens up the main system. On a blower with the carb mounted above the rotors there is constant vacuum all the time even under wide open throttle. The power valve will never open and you will have a lean condition. To remedy this there is a modification you can have done that is called manifold referencing the power valve. You plug the vacuum feed hole in the baseplate for the power valve. Then you drill a hole in the side of the main body into the hollowed out vacuum chamber for the power valve. You then insert a vacuum nipple in this hole. You will run a vacuum line to the lower intake manifold from the new vacuum nipple. Now you will have vacuum on the power valve at an idle, and when you hit the gas as the boost builds, it will force the power valve to open and richen up the main system. This can be done by most carb modifiers or even yourself. We offer quite a few different size blower carbs with this already done. Consult you local Holley dealer or our Techline for the correct application."
Here's what Holley has to say about ignition timing.....
"Blower engines like timing advance. If the initial timing advance is not enough it will cause issues. Most blower engines will run between 12-20 degrees of intial timing and a total of 30-32 degrees. You do want a fairly fast timing curve. All the timing should be in by 2500-2800RPM.This is just a guideline. All engines are different. The other main cause is a lean running engine. Make sure the carbs are tuned correctly for the setup and that there are no vacuum leaks. Remember the blower moves a lot more air through the engine so it needs more fuel as well!"
I went through the Holley site and found this technical info as well. I highly recommend reading through it a few times.....
If this were my project and I had no means of finding out what jets to run in the carbs, I would run the ones that came in the carbs out of the box, then I'd be on top of reading the spark plugs if I had not equipped the exhaust system with oxygen sensor(s). But just let me say here that if I were you, I'd be on the phone to the Holley engineers and I'd have every last detail of your combination written down and in front of me before I made the call.....
Holley Performance Products
You have far too much money invested here to be making guesses.
One last thought regarding air supply. When I'm asked about air cleaner requirements, I generally suggest 14" diameter by 4" tall for a naturally-aspirated street motor up to 406 cubic inches and 6500 rpm's. That gives the motor 175 square inches of filter area and insures that the air cleaner will not be causing excessive vacuum at the carb inlet. The motor has to inhale easily through a well-designed intake system and the motor has to exhale easily via a well-designed exhaust system if it is to make good power.
Your motor, depending on boost, could easily pass 1.7 times the air that a naturally-aspirated motor of the same displacement would pass, so if it were my project, I'd opt for air cleaner element area of 1.7 times 175, or 300 square inches. There will be others who will disagree with this, but that's the way I'd do it. Actually, I'd look for a large oval element to enclose both carbs and make my own base and top lid. Maybe a diesel element of some kind.