The factory 'balance' pipe you are talking about prolly isn't. Most of them are blanked off and are just there for strength.
Just stick with 4-1 if possible, nice and simple.
I've often thought of joining 1-4 and 2-3 too, I guess it may add a bit of mid range torque over 4-1 and makes more sense than 1-2 and 3-4.
What I learnt with balance pipes on v8's was to draw a line on the pipe with crayon, and where it first burnt off was the best place to put the balance pipe. I guess that applies to bikes too? I don't think the size and length of the balance pipe has a huge effect, at least the car guys don't seem to be that fussed about it.
Get the size/length right and it should run fine, and pick up quite a few hp in the process

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