Hi Andy
The length of the ram pipes has an effect on performance, ie the longer the pipe, the more low down torque you will have but at some expense to top end power apparently. Canam cars tended to have very long ram pipes.
I have got Jenvey throttle bodies on my car on a weber manifold with quite long ram pipes (no air cleaners) and have never had any clearance problems under the rear window. I also get a good view out of the back in the rear view mirror.
Chris