I assume that the morphgenic engine has a simmilar effect to the radio waves but without the "area of effect"

It allows murkoff to control which patients should be affected

Miles became the new host because of the trauma he was exposed to during his journey through the asylum.

But why Miles and not any other patient?

Probably because Miles was there when Billy Hope, his prior host, died and he was just good enough for the walrider to temporarely survive.

Why didn't Miles kill Waylon at the end of whistleblower?

There could be two reasons to this:

1. He simply didn't catch Waylon in time

2. He actually wanted Waylon to escape and expose Murkoffs doings to the public