OK, basically uncommenting line 1053 and commenting 1054 does its job, script looks like it should now.

OK, this is kinda unrelated to the main topic, but PTP is working as it should on newer versions of GreaseMonkey. Other addon used by me was breaking it.

In case of 3.4.1 and 3.5 I was using a fork, since versions higher than 1.15.1 don't work with Pale Moon: https://github.com/janekptacijarabaci/greasemonkey/releases/tag/3.5Fork

Re: @Marti:
I do not know Javascript at all, so I'm not exactly sure what you're meant here.
Currently I am using Greasemonkey 1.15.1, because one other script that I heavily rely on (Pixiv Translation Plus) seems to be not working on newer versions.
Changing that one instance of CloneInto with window.CloneInto just returns that it is not a function.

UI is broken in the exactly same way as it was earlier in case of Firefox versions >35
https://openuserjs.org/scripts/TimidScript/%5BTS%5D_Linx_Amender/issues/UI_and_script_loading_borked_after_upgrade_to_FF
This time however it happens only when using Linx Amender 3.0.25 or later with Pale Moon.

Error console shows this error when opening script preferences:

Error: cloneInto is not defined
Source File: file:///E:/PaleMoon%20Goanna/6kuy32jn.Goanna/gm_scripts/%5BTS%5D_Linx_Amender/%255BTS%255D_Linx_Amender.user.js
Line: 1054

   var names = cloneInto(GM_listValues(), window);

Confirmed with Greasemonkey versions 1.15.1, 3.4.1 and 3.5 and Pale Moon 25.7.3 and 26.0.0 beta3.
I am getting a feeling that that fix introduced with 3.0.25 is actually causing this.

Re:
Damn, that reply didn't went as I wanted.
I can get access to touch.pixiv.net after changing my user agent to one that resembles a mobile browser.

touch.pixiv.net was their mobile site and its dead.

I can browse it without any issues.

Most of the functionality of the script stopped working a couple of hours ago.
Direct links to images are not generated, manga works are not properly detected, search filtering doesn't do its job.
In error console of PaleMoon I'm getting a bunch of errors every second:
hotbox is undefined
local link to the Pixiv++ user.js file Line: 1990

The same situation happens on older version of the script (3.1.69) and on a different web browser (Chromium).

That whole mess has probably something to do with this: http://www.pixiv.net/info.php?id=2933

Currently links generated by this script are like this:
http://i1.pixiv.net/c/480x960/img-master/img/2014/10/02/00/31/41/46298198.jpg
Removing "c/480x960/", replacing "img-master" with "img-original" and adding "_p0" before the file extension will give you a correct link:
http://i1.pixiv.net/img-original/img/2014/10/02/00/31/41/46298198_p0.jpg