People are already running microsquirt efi on CB's so that's been done.
A diffuser style intake manifold works best in turbo applications to ensure all cyl's are fed air as equally as possible. It won't really work as well in a carb'd draw thru type set-up that a lot of the old school systems I've seen here use.
With a basic plenum style intake manifold you will get rich and lean cyl's depending on the path of the airflow into the plenem. A diffuser style intake manifold helps equalize the incoming air throughout the plenum before it enters the individual ports.
Sorry, I've been up close to 24hrs and I'm having a hard time putting it into easily understandable words.
1st pic: Top smaller tube is where air will be entering. Bottom bigger tube is main plenum and will be capped.
2nd pic: Plenum is capped off and intake pipe is attached. On this particular manifold space constraints required the intake tube to actually have to be notched into a corner of the plenum. Not ideal, but still best compromise.
As far as headers go, a custom ss header wouldn't be an issue either. I actually kinda liked the basic header design on Greggos new turbo project bike so I would start there as a basis for the design.
3rd pic: Example of ss header we build for 4cyl 8v Volvo's.