jp wrote:The boss bonus numbers were time based if I recall correctly. And then the multiplier you had would obviously multiply to points for killing each form (hence why boss fights were the big score bringers in the original).
But I'll check it out today and try to figure it out for sure.

No, they decrease with time, but the initial 'new' value has a dependency on your item counts.
It works like this: when the boss fight starts, the initial bonus value is set to item_count * 360 (you can verify this at the beginning of the boss fight, top right corner under the life bar)
This value starts decreasing as soon as the battle begins. It will INCREASE if you pick up items, but you need to pick a bunch up to have any useful increase (more later)
When you destroy a boss form the current value of the bonus is added to your score (the big number displayed on the screen), the NEW value for the number is then current_bonus_value + (item_count * 360). If you've timed it right you also converted a bunch of bullets to items, when you suck those in they will increase your bonus value too, although I do not know the formula. On really dense patterns I've seen it increase by a few million.
If you destroy a boss form with shot, you get no multiplier based bonus at all. If you destroy it via a thrown enemy, it acts as normal and you get enemy_base_value * multiplier added to your score.
All this appears to hold true in the XBLA version, the difference being that we don't really know how the multiplier works anymore.
If it's directly proportional to your item count you want to play the boss fights like you did before, with only one change: you should take every opportunity you can to destroy a form with a thrown enemy since there's no penalty for doing so. You'd still want to milk the boss for as many items as possible.
If the multiplier is dependent on something else, then you may need to modify the boss milk type strats; although I can not think of a scenario where you wouldn't want to milk the bosses for items.