Pairing odd cylinders is not a wise choice because what happens is that the mixture gets pulled through the carb twice in quick succession. That's not enough time to clear out pressure pulse at higher rpm's. You won't find too many performance applications that do that, but there are countless examples of it being done. Most of the twins you do see it one where you can pull good beans through them are 360 twins where the problems becomes substantially less of an issue.
If you want some math behind it, just consider this:
- Firing order is 1-2-4-3, and because all the cylinders are identical the intake order is also the same (just lagging behind the point of firing based on the cam specs).
- Stock cam duration is something like 220 degrees @ 50 thou lift, so for 220 degrees of crank rotation the intake valve is open to some degree
- Based on this, cylinder 1 opens it's intake valve, and 180 degrees later cylinder 2 opens it's intake valve as well, but because the valve was open for 220 degrees you end up with both cylinders drawing concurrently through the carb for ~40 degrees of rotation. Also consider piston 1 is slowing down at the end of the intake stroke and the vaccum in that cylinder has dropped, while piston 2 is pulling strong vacuum.
- Tack on a big cam and this problem becomes worse. Different carbs will handle this situation differently as well.
I could go on but you get the point I'm sure. Problem disappears when you draw from 1 then 4 because the offset becomes 360 degrees which is longer than the duration. Same problem exists with a 180 twin vs. a 360 twin (as I mentioned before).
Note that most CB750 twin carb setups also use this same approach. Obviously YMMV, but there's the counter argument.