How can I customize keyboard shortcuts in Thunderbird?

Keyconfig allows you to configure keyboard shortcuts.

Read more about it here.

Update 07/2020: Your best bet for custom keybindings currently seems to be: tbkeys. Follow the instructions there to get keybindings, customizable within a file in your user-home directory (see here for cmd references [PR created to include in README.MD]).

Update 12/2019: As of Thunderbird 68 dorando is currently not supported anymore. A good (deep dive) source of current development can be found in the mozilla forums or directly at the github of the dorando project.

OP:

Seems like the original keyconfig from 14 years ago is not compatible anymore with thunderbird 60.0 and up.

dorando-keyconfig is the official new supported version as far as i can tell. Some descriptions seem to be missing, but not a big issue (i.e. "Mark > As Read" is key_toggleRead).

Thanks to dorando and the new maintainers for keeping up the good work .

You can unzip Thunderbird's chrome and edit the .dtd files within them, which usually contain the key bindings, if you want something that's not extension-dependent. Here's an example from a DTD file for my extension:

<!ENTITY removedupes.remove_duplicates_menuitems.remove.accesskey "D">
<!ENTITY removedupes.remove_duplicates_menuitems.set_originals.accesskey "o">
<!ENTITY key-removedupes.modifiers "alt,shift">

this is of course much less convenient than using KeyConfig, but that's the low-level non-dynamic way to do it.