Who were some of the best boxers in history with some of the lowest knockout percentages?

Historically, Floyd's KO% of 54 is actually pretty healthy. The majority of pre-WW2 champions/top boxers had far lower percentages.

For example, looking at Ring's end-of-year ratings from 1925, only a few of those won more than half of their total fights by ko. More specifically, if we take the Top-10 in each of the 8 original divisions (a total of 80 boxers), only 5(!) retired with a 50+ ko percentage:

Godfrey 64.29% (81/126)
Berlenbach 62.96% (34/54)
Dempsey 59.46% (44/74)
Tunney 56.47% (48/85)
Wills 50.45% (56/111)

https://boxrec.com/media/index.php/The_Ring_Magazine's_Annual_Ratings:_1925

 

Total number of fights.