Oh, wow, it's been a busy day.
So, as others have pointed out, the first thing you have to understand is who has say over what. The rulebook tells us that we have say over when effects that affect objects we control occur. So, it doesn't matter who controls the effect, but rather who controls the object being affected. If my creature is burning, I have say over that burn damage (as an aside, it should be mentioned that nobody controls Conditions). If my creature is regenerating, I decide when it regenerates. If my creature takes damage in any way, I decide when it takes damage.
With this system, timing issues are pretty rare. Initiative never gets to decide when their opponent applies an effect. Instead, what they are deciding is when their own effects happen relative to their opponent. Does mine go off before or after theirs? That's it. That is the entirety of the power bestowed upon initiative. Deciding relative order.
Effects like Death Link can cause confusion because it appears to be affecting two different objects which may each have a different controller. The catch is, that these are actually the same effect. They are linked and have to occur at the exact same time. You can't break them apart. On top of that, the card itself makes it clear that the controller of death link decides when the effect occurs.
So, what we have then is Player A deciding when to use Deathlink, and Player B deciding when to regenerate the creature that has Deathlink attached. Since the relative order of these two events matter, we have a timing issue that gets resolved by Initiative. So, if Player A has initiative, they may say that they heal before you regenerate, and their healing just happens to kill your creature before it can regenerate.
Whirlpool, in my opinion, is a lot easier and more straightforward, but I feel obliged to comment on it since I'm the one who wrote the supplement entry and it appears like it wasn't quite clear enough. If player A controls a whirlpool, they decide when to remove the Dissipate tokens from that whirlpool. If player B controls a creature stuck in the whirlpool, they decide when their creature takes damage. Initiative decides when these two things happen in relation to each other. This is all part of the normal rules. Nothing special going on.
So, if Player B has initiative, they can't force Player A to resolve the effects on their objects in any specific order. Player A can resolve as many effects as they want on their objects before and after resolving the whirlpool, in whatever order they so choose. However, Player B does get to say when effects happen to Player B's objects in relation to Player A's, and can say that his creature doesn't take damage until after whirlpool's dissipate is removed. Which would avoid the damage all together on the last dissipate since the Whirlpool would be destroyed.
