Ok, this has been an adventure.

First of all, here's the link to the updated Chapter 2:
http://ge.tt/9UcFtAE1/v/0?c
I used ge.tt because the other uploader was too darn slow today for some reason. Checker says the duration is 28:26:95, the file size is 26.0 Mb, and the volume is 89.3 dB.
Hopefully all is fixed now, but let me know if it isn't. I decided to try to isolate and fix the clicks myself, because I think I should know how to work around this problem.
I checked the samples in the file you posted. I could see exactly where you made changes, but unfortunately I could hear no difference between your edited and my unedited versions.
I watched the youtube video by Phil Chenevert, and had no trouble following it as it's exactly what I do with stuff I can hear. But... I couldn't hear most of the clicks he was editing out either.
I listened to those two places you identified on two headsets, two ear buds, my computer speakers, and the TV, and I couldn't hear the clicks on any of them. So, unless you and Phil use higher-quality headphones or speakers than I currently have access to, the limitation is in my ears. I think the problem is more likely to be volume than frequency. Speaker sensitivity at very low volume is a measure of its quality (and it's also a measure of ear quality, alas).
That you and Phil can pick one out a click in the middle of a spoken word is (to me) a remarkable skill. I'm certainly not going to deprive myself of the benefit of it by asking you not to point these things out any more. I'm sure many listeners will appreciate the resulting improvement in quality.
After some thought, I came up with this solution. You could PL the files in Audacity, and whenever you hear a click, stop, zoom in until the track time is displayed in milliseconds (three decimal places), and note the precise time of the click in the reply you send to me. If I go there at the same zoom level, I should be able to see it even if I can't hear it. Does that work for you?