I think you're right about the torture scene, and that if you looked carefully at production pictures you could barely see the uniform sleeves under his bare body (yipe). I looked the clip up on YouTube though and it's of such poor quality you can't really make anything out. Still, when he was beamed back to the Enterprise he was in the latter TNG uniform as he was whence abducted.
As for the shuttle scene, THAT YouTube clip was clear enough to show Picard and J-L in the DS9 style with Worf still in TNG duds.
Mark