On Thunduros, I agree with losing Taunt, but definitely keep Discharge. The 30% chance of paralyses, plus a chance of hitting both opponent 'mons is too good to pass up. But yeah, Substitue over Taunt seems better.
Running all physical on T-tar I would usually disagree with, but in your case, I think it would be better. Thunduros and Ninetails hit reasonably hard on the special side already, and without at least Close Combat on Hitmontop, your physical attacks throughout your team are severely lacking.
Brave, 0 Speed w/ Iron Ball hold item is what I suggest. Rock Slide, Fling, Fire Punch, Protect seems like the best set for your team.
Rock Slide hits STAB on both opponents Pokes.
Flinging the Iron Ball gives you a STAB 130 base power attack. It's only one time use, but hitting as hard as T-tar does, you really only need once.
Fire Punch gives you a pseudo-third STAB, in case you are forced to bring in Ninetails after T-tar, but while T-tar is still on the field.
+char