There is no handling of international and loan words' pronunciation of 'o' (which may use ɔ)
No distinction between long vs short phoneme lengths (e.g. 4.8c in Ambrazas)
Degemination only in cases of exact repetition of consonants, although in reality degemination often occurs in other cases
I did not quite understand the part about affricates being replaced before front vowels (4.6)
Based on one of the given examples for aspiration of final /t k/ (kasmẽt,) I ended up guessing (but without high confidence) that the aspiration (or combinations of multiple consonants in general) functionally adds a syllable and turns the relevant vowel into a "non-final"
Perhaps most consequentially (relevant to realization of 'a' and 'e' vowels) it is naively assumed that all stresses are explicitly marked with a tilde or grave or acute diacriti, though this often seems not to be the case outside of scholarly/academic/reference texts
Sources: Wikipedia (+ to resolve notational differences), Omniglot, and Ambrazas et al. 1997 book, Lithuanian Grammar. The Ambrazas book was my main source.
Some known issues/quirks: