You can search for optimized lower intake, perhaps in the performance section since it's not a 3 liter specific mod. I know someone has it done and posted pics. IIRC, they noted small gains.
To get your last 3 screws out, use a small tap hammer. The rails will slide out (assuming they're clean) once all of the butterflies are removed. Since I never planned on keeping mine, I just drilled out the stuck screws.
