In my opinion, tuned port, pressure waves and runner size can be tossed out the window when you go from naturally-aspirated to turbocharger-aspirated. All you will need is a plan to deliver the proper air/fuel ratio to the motor and a way to keep the charge cool. In your case, using FI simplifies keeping the A/F ratio in line. I like your "over the top" runners, same as the intake system on my old '91 Ford 300 six cylinder motor, but I think if I were doing it, I would fabricate an intercooler to fit in that space also.
I understand that you have little room on the driver's side for the turbo unit, but weigh making room there by doing a little surgery on the existing parts against running exhaust tubing to the other side of the motor to run the turbine. I have made the comment many times that with a cutting torch, a Sawzall, a MIG and a good hand grinder, you can make anything fit anything.
I think if I were doing your project, I'd mount everything on the driver's side by doing some surgery, then I might mount an air-air intercooler down low in front of the car.
I'm certainly not the forced induction guru on this board, just presenting a few thoughts......good luck.....