How can I type Lithuanian stress characters (e.g., ą́, ė̃, m̃)?
For info on how to add combining diacritics to any character with ABC Extended, see this page

http://sites.psu.edu/symbolcodes/mac/codemacext/

For example, m̃ is made by typing m and then option-shift n. ė̃ is made by typing option w, e, then option-shift n.

The keystrokes for adding acute  ́ and grave  ̀ are option-shift e and option-shift `.

You might want to create a customized version of the Apple Lithuanian keyboard using Ukelele to adding keys for the combining diacritics used to indicate stress.  Here is one you can try.