You should really consider keeping the variable intake system. You are already modifying your car by swapping to an engine that was not available when new. A minor indentation in the firewall is trivial compared to that.
I spoke at length last week with a local guy who swapped a 5.7 into his Javelin. He also put a 392 intake onto his engine and kept the variable runners operated through an adjustable "window switch" set at 4500 RPM. He says he can definitely feel the added power when it kicks in. Similar to hitting the NOS switch. Since you are going with a 6.4 you obviously wanted big power. No sense leaving it on the table. Curt has done the leg work on this.
Wow, you guys like my stuff! Hahaha
Im just gunna say all that work i did, everything was worth it.... it drives like a dream! Took it on a 1000ish mile road trip this weekend