1. The tones won't change. the in-menu lead guitar tone (tone slot 1) get swapped out with the base tone at the start of the song, but that's it, the wah-wah and distortion never kicks in. I've followed this tutorial and done exactly like him. https://www.youtube.com/watch?v=RtAzj3618wk

2. how do I place these in EoF?: pinched harmonics, vibrato sustains, hammer on and pull offs?

1.  Use "Track>Rocksmith>Tone change>List" to make sure your tone changes are listed and at correct times.  Whichever tone is the default will have "(D)" listed next to the name.  If none of them are listed as the defualt tone, use "Track>Rocksmith>Tone change>Names", select the appropriate tone and click the Default button.  It's also worth going to the Names dialog to make sure there are only the 3 tones you describe listed here.  If any of them were added with a typo or incorrect letter case, it ends up being exported as a different tone that has to be defined in the toolkit.

 

2.  You can turn selected notes into pinch harmonics with the "Note>Rocksmith>Toggle pinch harmonic" function (or use the SHIFT+H shortcut).  You can apply vibrato technique with "Note>Pro guitar>"Toggle vibrato" (or use the SHIFT+V shortcut).  You can set hammer on or pull off technique with functions in the Note>Hopo menu (or use the H or P shortcuts).  All of these techniques can also be set by selecting the note and using the "Note>Pro guitar>Edit pro guitar note" function (or use the N shortcut).

Thanks for your help, @@raynebc! One last question: are there other places than Songsterr you can get tabs with .gp3, .gp4 and .gp5 - files?

There are tons of websites, but quality seems to vary from song to song unless you got to one of those sites that charge money for tabs.  You can usually Google the song name and "gp5" or "guitar pro" and find lots of options.