Effects on the attacking Pokemon are applied before weakness and resistance. Effects on the defending Pokemon are applied after weakness and resistance.
The contents of your deck are technically unknown. If an effect calls on you to search your deck for a specific card or category of card, you may choose not to find a card, even if it is present in the deck.
Source:
Worlds 2006 PCL Announcement (2006-08-18), PUI Rules Team (2008-05-08)
The game has no knowledge of the contents of your deck. For example, if you search your deck for something and fail, you can still use other cards or effects to search for the exact same thing.
An attack that copies another Pokemon's attack can only copy attacks printed on that Pokemon, not other attacks that the Pokemon may use due to Poke-POWERs, Poke-BODYs, Stadiums, etc. (with the exception of Lv.X Pokemon since they are considered "extensions" of the original Pokemon).
Benching a Pokemon removes all Special Conditions on that Pokemon including Poisoned and Burned, and all Attack effects on that Pokemon that do not place a Marker (such as Imprison).
If a Retreat Cost is set to zero by an effect, it cannot be increased. Note this is different than a Retreat Cost that was reduced to zero by subtraction.