Part of the game. A lot of MKIV guys do the same with aftermarket intake manifolds like the Hypertune.
I had to relocate the battery in my MK2. Wasn't a decision I regret at all. Just no way to fit such a huge manifold, unless you start moving other stuff around. Plenum volume, angle, and throttle body size. I really want the performance of a better manifold over the factory 1JZ.
Sound Performance's 7M FFIM definitely looks like it is for the very serious of tuners, just like Hypertune, Pro-Jay, etc.