My stock software version is 1.54.707.7 (Asia Phone) & stock radio is 1.16.2133156.UA10G.
In my own opinion (& I have no proof to back it up), I guess the clicking/popping noise from the speaker happens after upgrading to 1.54.401.10_firmware which has the radio 1.16.2133156.UA15G.
The noise comes & goes. It's hard to replicate it. It is quite obvious in poor reception areas & I get drop calls too.
My wife's m8 is still running stock radio & she says she doesn't have this issue. So I've just pulled her radio.img & flashed it on my phone.
I will give it a few days to see if it's the radio or not.
The next step is probably warranty it.
I had this issue so badly on the m7, so when I first bought the m8 I tested it thoroughly to make sure it doesn't happen to me. & now it does
Any advice is greatly appreciated.