Just Jap Intercooler kits DON'T line up, never did. I did mine 2 weeks ago and it is the biggest pain in the ass- but once finished it is so good to look back and say, there, I'm so proud of doing that myself..! All my brackets were custom, the pipes never line up and I had to get an extra silicon elbow for 40 bucks from Autobarn that fitted.
I used the 'normal' kit not the return flow one, so had to drill a hole under battery tray.