Spiritomb

If my opponent has a Ting-Lu ex with "Cursed Land" Ability active and a Gapejaw Bog stadium in play, when I put Spiritomb with the "Fettered in Misfortune" Ability into play is there a brief moment where Spiritomb's Ability is active before the damage counters from Gapejaw Bog are placed onto Spiritomb which in turn triggers "Cursed Land"? For example, making Honchkrow V with the "Boss Pockets" Ability discard all but one of its Tools before "Fettered in Misfortune" turns off?

The order of effects in this scenario are as follows: 1) When Spiritomb is played onto the Bench its Fettered in Misfortune Ability immediately cancels out the Boss Pockets Ability of Honchkrow V, thus causing all but one of the Tool cards attached to Honchkrow V to be discarded. 2) Gapejaw Bog's effect puts damage counters on Spiritomb. 3) The Cursed Land Ability of Ting-Lu ex cancels out Spiritomb's Fettered in Misfortune Ability.

If my opponent has Spiritomb with the "Fettered in Misfortune" Ability in play, does attaching a Fusion Strike Energy to my Genesect V allow it to use its "Fusion Strike System" Ability or not?

Fusion Strike Energy protects Genesect V from the effect of Fettered in Misfortune, so yes it would be able to use its Fusion Strike System Ability.

If I attack Maractus that has the "Exploding Needles" Ability with a damaged Lillie's Comfey's "Fade Out" attack, would I put 6 damage counters on Lillie's Comfey and knock it out before it goes to the hand?

No, Lillie's Comfey would go to the hand first and then Exploding Needles would be triggered and find no valid target.