Hi, just a rules verification:
If Ditto is Transformed into another Pokémon with at least 60 HP, and with at
least 5 damage counters on it, would Gust of Wind Knock Out Ditto? The card
says that Transform only works when Ditto is active, so when it goes back to
the bench, it becomes Ditto again, correct? And because it is now Ditto with
50 HP (Transform shuts off) at least 5 damage counters Knocks out Ditto?  I
am almost sure this is true, but I'd just like to get this confirmed. Thank
you for your time.

-Will
(raiden9984@aol.com)

Well, yes.  As a matter of fact, I knocked out 2 Dittos in a tournament the other day that way.  Once they have 5 or more damage counters on it, Gusting it to the bench will knock it out since it becomes a Ditto again.

Scott