I just try to explain the second one:② 我等他等了三个小时。 In my opinion, "等他"is the known or less important information,while "等了三个小时" is the new or more important information. And sometimes we have to use this structure otherwise there will be something wrong in grammar: right：他说汉语说得很流利。 wrong：他说汉语得很流利。 当然，也可以说：他说汉语很流利。

right，This 3 sentence have the same meaning！but，there is a little difference! In china, we like emphasize something when we are talking! So,sometimes we use some words to emphasize! For example:就and才！and sometimes we use the different order to emphasize.for example:① 我等了他三个小时i want to emphasize:I wait ! ② 我等他等了三个小时i want to emphasize: the time that I wait him! This is a grammar!( S+v+o+v+time) ③ 我等他有三个小时I want to emphasize: three hours! So,my English is not very good, I don't know you can understand or not! I hope those words can help you!

For ③ to be correct, you would need a "了" ex. 我等他有三个小时"了"

The three phrases make sense to me. However I would say ③ 我等他有三个小时 is not normally used in colloquial speaking. The slightly difference between ① 我等了他三个小时 and ② 我等他等了三个小时 is in the emotion. The second one seems to have more emotion in it since it express the 等 twice.

o me respondes en chino o ná! xD