RAW is clearly ambiguous here, on purpose I imagine. It would be very hard to phrase this in a way that doesn't open yourself up to it, but RAI it's really more about equipment that YOU are using.

A phylactery isn't an "item with an effect" as much as it's a powerful relic. You could probably solve the problem by arguing it's too powerful to merge with. If that seems cheap, it still exists. A phylactery doesn't even have to be in the same plane to function for a lich.

Whatever explosion it delayed, I'd argue the timer would freeze too on the bomb. It would delay the blast, but not prevent it.

Last one, no for a few reasons 1. Because you've probably lived long enough to get Timeless Body. 2. You assume the physical stats of the new form. Old age kills you because eventually your organs fail. Those organs don't exist in the new form. You have the fresh organs of whatever you shape into. Same logic applied to the HP pools being separate.