When a card says "Any player" does that refer to yourself ? Like the d6 item for Isaac for example..can you activate it to re roll your own rolls?
Yes, any player includes yourself.
When a card says you can destroy an item in play is that including your own?
Presumably yes as long as it doesn't say something like "another player".
On the Bum Bo card when you hit say the the second or 3rd ability do you just get that ability or each one before it as well?
You get each one before it. The card says x+, meaning that many counters or more. That condition is still true when you get to the 2nd and 3rd thresholds.
Any time a card says to take or gain a treasure card does that mean off the top of the treasure stack or do shop items count as treasures that can be taken?
It's not in the rules but Edmund said you get it from the top of the deck.