Cold air intake Question?

[T-Dubya]

I have a 93 4runner 3.0, and have been thinking about fabbing a cold air intake, mostly because im tired of dealing with vacuum leaks from the dry cracking factory setup. Ive been looking at other peoples setups and notice most take out the resonator box and plug the (PAIR) hose, I was wondering If you disconnect, and plug the vacuum hoses from the intake, VSV and so on, And what effect this has on the engine? Any help would be appreciated Thanks.