Getting back on topic.
Watching Ali's fights, both early and late, is to re-appreciate, if that is a word, how fast and accurate his punches were, and how good he was at slipping punches, often by sliding his head backwards while keeping his long arms still in jabbing range. Here is a link to the Ali-Liston fights, Liston was a terror who had knocked out all before him, and he could hardly manage to land one on Ali.
https://youtu.be/NXYwb2C6Hec
Now imagine Lee, with his much shorter arms, trying to connect on Ali: Lee would be getting hit constantly while trying to reach the much bigger man. As for kicks, a kick takes so much longer than a punch, and frankly Ali's reach with his arms wouldn't have been much shorter than Lee's reach with his legs. Ali was criticized for supposedly not being a very hard hitter, and it is true that most of his KOs were TKOs, but that is against big men who could take heavy punishment. Against Lee, Ali's punches would have been flattening.
Again, that assumes blows only above the waist, as the OP posited.