I own a solid running but rough body CL S, was maybe interested in swapping the drivetrain into a civic or integra. I'd prefer a sleeper, so no manifold through the hood. I know this can be achieved on DC integras but can it be done in an em1 or ek?

 

Short answer is yes.

But you'll need to be stock height

 

there are also options for adding clearance to the top of the engine with something like this or this. both seem a little pricey for your purpose, but i'll let you decide how you want to spend your own money...

a potential alternative is to grab an upper plenum from a FWD VQ (Nissan V6) or 1MZ (Toyota V6) and have an adapter made to fit it to the J32 runners. The VQ has it's runners more in line so the 1MZ would probably be the closer match.