I thinks it's SolidWorks you can do this with. I know there is a design/modeling program out there where you can draw up a design and test it with in the program, flow properties with current lines and such. Then you can adjust runner cross sections, lengths, etc by simple clicks and it can overlay the results. Far as I had heard you could also model an existing engine design and put your product on that engine and run it and it would show gains. No it's not a desktop dyno thing either, way way way better.
But I would say to stay with a tubular design, in the 8" to 11" (high rpm, about 6,000 or better is where it would really shine, longer runner = lower rpm range) range for runner length from the back of the intake valve, keep bends to a minimum but keep the entry angle to the head about the same, a small plenum is all you really need (simply to hold a nice set of radius'd runners/bell mouths).
The larger the plenum volume the less affect throttle body placement will have. So this is one thing I would definitely play with in the programs.
Far as any other dimensions you need go, it will depend on your intentions with the car, if you wish it to fit somewhat like stock or if you are moving some things around.
lol, I post then randomly think of the program, Pro-E I believe it actually is.