EDIT: Stage 2 boss - second phase rotating balls (~50+mil), final phase (~50+mil)
Damn, sounds like you have to cash-in on the balls and then go through the 2nd phase 1 or 2 more times in order to milk enough gems to cash in for the last phase... so risky but totally sounds worth it.
Yes, the stage 2 boss takes some practice, but becomes routine after awhile. You can get over 100mil on that boss alone, so it's a must to learn how to milk it if you want a good score.
Basically in phase 2 you fill up on gems in the first set of balls to max your multiplier, cash in the x9XXX multiplier on the second set, then fill up on gems on the third and final set (it fills you back up to 9999). You have to time the destruction of the second phase to coincide with the destruction of the third set of balls, otherwise it won't work. Then you have to use this multiplier on the SECOND loop through all of the last phases' bullet patterns. I usually bomb at the end of the first wave (or 'bullet loop'), but pros can manage to navigate through it without a bomb. Still, one bomb and scoring on the second loop with a x8XXX multiplier gives more points than scoring at the end of the first loop with a x9999 multiplier, so it's worth it.
Ah, very good info here! This is actually (mostly) what I came to ask about. I was actually hoping you had some idea of how to dodge the S2boss's 3rd form whirly pattern, but I suppose I'll be bombing it, too

I'd also guess that, since the hitbox is longer than it is wide, it would be a better idea to dodge the 2nd form's balls' shots vertically as opposed to horizontally? I haven't tested this much, though.
About the stage 4 boss: As soon as I learned how to NMNB (or NM1B? don't remember) the stage 4 boss (Maniac), I quit playing, so my memory is hazy, but do you have any tips for timing the huge-scoring pattern? I was never able to get it properly, though I may just have needed more practice.
For the falling balls that shoot out more falling balls, I had some kind of loopy little pattern where I'd dodge near the bottom-right corner, but is there a widely-used, consistently safe pattern for that? That pattern sucks.