That is one of the draw backs of trying to build a custom exhaust. Things like X pipe size inlet angles and depth along with placement of the x control the overall pitch and tone while having a big impact on power.
Going 3 inch with 4 inch mufflers cost you hp and adding a valve up stream will just end up taking a big tole on any improvements out of the equation.
I made a big exhaust post Ill try to find it. I actually had a chance to see Roush raceing testing exhaust systems for there NASCAR car and other race cars for road raceing one week. It was eye opening and Iearned a lot
With 4 inch mufflers the air is going to be tumbling around and around as your not going to have enough CFM to fill the chambers and resonation will take place. The best way to see if you have a exhaust that isnt flowing properly is to rev the car and see if it back drags on decell. with 4 inch mufflers on a 3 inch system that most likely is the case.
The best fix is get the proper size mufflers. If you dont want to do that try getting resonators. The fact that you have a big system already you might want to go with longer resonators. But make sure the resonators are 3 inch and no bigger. The longer the better.
I went in a ride in Countvohns S8 with a 3 inch and you can see the video he made. Its tame down low and mid range with ZERO drone and cabin effects. But I know they had to make a few revisions with the X to get more power and control the noise. I know he put resonators in the system as well. The exhaust is very well done. Proper noise WOT but crusing and low speeds its a just noticeable hummmmm…
Before you put the cutout in I would strongly suggest getting resonators put in up stream of the x and keep the back ones. or get the proper size muffler on
you mean the tips are 4 inch?