Are repainted/modded figures still tourny legal as long as they are on a non modified base/dial?

Yes. It really isn't any different than playing a flier's base without the flier attached (stupid Archangel can't stay upright...).

As I understand it, as long as it's the same figure (ie Sinestro on a Sinestro base) you are fine. The problem arises when you try to play a custom sculpt. I could be wrong though.

The official answer is...asking the Envoy running the event. WK has specifically left this section of the rules vague so that each Envoy can do what works for them and their event.

The general rule of thumb that the Envoy should be using is: Is the character confusing to your opponent? If the opponent can tell who it is easily...there shouldn't be a problem. If the opponent complains because it is interfering with their game...then the Envoy should disallow the mod. So it could also vary from game to game in a tournament. (And of course you should always make it clear what character a mod is before the game begins.) So just check with the Envoy. Also many Envoys, myself included, ask that you have the regular version, unmodified, of the character on hand just in case there is a problem.

I wanted to take Green Arrow and put his head on Ult. Hawkeye's body cuz the current Green Arrow looks dumb. I was just curious though cuz my friend said if it was legal people would just put all the same sculpt on different dials to "throw off" the opponent. But I figured you can still look at the name on the base.

See above.

Generally an Envoy would not allow you to just stick Archangel on a GL base to confuse your opponent. Or to glue Captain America to a Hulk base to confuse your opponent. But this is all left to the Envoy to decide. Looking at the name on the base is not going to be enough if the Envoy feels it would confuse your opponent.

So with what you are doing...ask the Envoy if they have a problem with the modification and bring the normal one along just in case.