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If you're speaking of the canon stuff that PL would allow, the only major thing I could think of is Michael Dooney's "MASKS" issues #46-47 where the Turtles travel back in time to ancient Japan with Shogun Chote. However I can see why it wasn't used as it would conflict with the backstory of Ch'rell taking over the Foot Clan in the 2k3 universe.
A few other one off stuff wasn't adapted like Gosei Hattori's entire character and stories, and of course they couldn't do any of Vol. 4 as it was just coming out at the same time 2k3 was.
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