I can't really hear anything that I'd describe as 'booming' in your original video?
There are really only two ways for an engine to make booming - induction or exhaust. If it's induction, then you need to look at what is not meeting the original design spec, because I think that you've got some sort of resonance going on. What's too stiff or too soft, wrong length or diameter. Engineers do spend a fair bit of time designing this stuff out - it's not pot luck.
You should also look for anything restricting the system, anything coming into contact with chassis/body/engine that might be changing the sound. As an example, think of a string on a violin and the enormous range of noise that it can make simply by changing the number of 'waves' in it. Same violin, same string, same tension in it. Just a different free length.
If you can capture the boom in another video it would help.