"No weapons, just hand to hand. Strikes
above the waist"
That's basically kickboxing rules.
Ali wins.
Ali was much bigger, heavier, taller, with a much longer reach than Lee.
Ali had comparable, or at least competitive, hand speed.
Ali could slip and block punches with the best of them.
Ali's punches would be harder than Lee's. Probably much harder, based on relative size.
Lee's ability to kick wouldn't be a deciding factor. Kicks are too slow for a fighter as slippery as Ali, especially when Lee has to launch them from far away at a much taller man. (As an aside, in kickboxing, fighters don't actually kick very much, and their most common kick by far is a "low kick", a low kick from Lee wouldn't put Ali down but Lee would be in easy range for Ali.)
Lee's ability to slip, block, and absorb punches is,
afaik, unproven.
Finally, Ali was a real professional fighter, Lee chose a different path - just as amazing, but different.
Honestly, I think Lee's chances against Ali would be no better than a great welterweight vs a great heavyweight.