you want the pistons to run longitudinal to the frame otherwise the motor will need shaft drive and interfere with pedals.
Barrels will need to be offset by thickness of the center crank flywheel.
I studied diploma of mechanical engineering 20 years ago, and was good with CAD then, but have not used it since, otherwise I'd draw up a few Ideas for you.
Still I might sketch up a few things.
I have an old shaft drive quad rear end that would be fun to do something like that with a transverse mounted boxer.
There is a thread here somewhere where a guy has an inline boxer in a pushbike frame.
What I would really love is a morgan style cycle car with a boxer twin mounted up front.
Have a look at a DLE 111 twin.