TheWertle has managed to translate the changes to Donald and Goofy in Kingdom Hearts II: Final Mix from the original Kingdom Hearts II:

• There are 7 additional “Get” bonuses for Donald. One time during a “Get” bonus, his HP will increase by 4 rather than by 3 for the rest of them.
• The Absent Silhouettes, Transport to Remembrance Battles, and Terra (The Enigmatic Soldier/Lingering Spirit) all give HP+3 except for Larxene who gives Item Slot +1.
• Experience needed up until Level 3 is increased. (Level 2 - 40 Exp, Level 3 - 86 Exp)
• It takes 60 seconds to recover from being unconscious.
• In Christmas Town, he has a different and new costume on from when he’s in Halloween Town.

• There are 7 additional “Get” bonuses for Goofy. One time during a “Get” bonus, his HP will increase by 5 rather than by 4 for the rest of them.
• The Absent Silhouettes, Transport to Remembrance Battles, and Terra (The Enigmatic Soldier/Lingering Spirit) give HP+4 except for Zexion who gives Crisis Half, and Lexaeus who gives Item Slot +1.
• Experience needed up until Level 4 is increased. (Level 2 - 40 Exp, Level 3 - 86 Exp, Level 4 - 146 Exp)
• His starting health is increased from 25 to 28.
• Time to recover from being unconscious raises from 35 seconds to 45 seconds.
• In Christmas Town, he has a different and new costume on from when he’s in Halloween Town.
• In the Pride Lands, “Shell Spin” will only make him spin around once.
• Also in the Pride Lands, when running, if he bumps into an enemy he does damage.