The Thunder 40106A is specifically made for the hyper charger. Thunder also state that the vacuum line may be left off with no impact on performance. I guess the flaps would have to be removed or left open
It would be a good idea to ask them what they suggest though.
One of the reasons I opted for a combination of a ThunderMfg adapter and a spike air cleaner is that it stopped my knee from hitting the air cleaner. If you like the old school look of the velocity stack take a look at Gar's write up on his 2 barrel air cleaner, it combines old school cool with improved comfort.