sorry for taking this time to get back to you
applications config files/folders are not the problem (and are not those almost for sure that are causing these issues):
are safe to keep (and /or backup and restore afterwards)
ofc you'll add here any specific app that you use (you mentioned tomboy; should be one safe as well)
the issue are the system config files/folders (as opposed to the applications above): those can/will be troublesome.
and as a foot note: why (re)using a previous HOME is nowadays more problematic than it was say until one year ago?
- until one/one and a half year ago gnome was evolving quiet slowly (the 2.xx was up for ages) and most of the code was fairly compatible >> this scenario is not true today anymore: gnome is evolving at a fast pace (a major release every 6 months)
- furthermore (and to add to the problem) until then we had 1 gnome shipped more or less tweaked in all major distros; today we have gnome proper, unity, cinnamon ,pantheon soon (and we can add mate to the mix) all with different config (and sometimes incompatible