I would like a shot at answering this question.
In the end, you are going to want maximum discipline where you can get maximum discipline. No matter what you have elsewhere, this entire build revolves around discipline. If you have to choose between discipline and % damage, choose discipline. If you have to choose between a "few discipline" and % damage, choose % damage. If you have to choose between 7 discipline and % damage, choose the increase to discipline while farming for another weapon of your choice with a % damage modifier but never take away the complete amount of discipline for % damage.
I would suggest that if you are more than 4 discipline away from the max discipline roll then always roll higher discipline. 5 discipline, as an example is 75% increased damage to your Multishot. 4 at 60% could probably be matched by 10% increased damage. At least that's what superfast in the head math tells me.
In your examples:
1) % damage without question.
2) This one is easy in my head but difficult to explain (sort of)... if you can roll through the rift while keeping max discipline the entire time then rolling the 3 discipline is FAR superior than 15% multishot damage. Heck, to be frank I can't ever think of a situation where 15% Multishot damage will ever be better than those +3 (45%) discipline. The reason is because with that 6pc bonus the 15% Multishot damage is 100% always affected by your discipline in the first place. You literally would need to be shooting your Multishot at 2 discipline in order for 15% Multishot to equal the damage increase as the 3 discpline simply because the Multishot bonus is affected by the 6pc.