What you've put together is a truly impressive and comprehensive piece of work!
However, if I make make a comment (not a criticism!), some of the feature you listed are the consequences of some general Polish rules, which are not specific to the locative case.
Of course what you've done is not wrong, and it's always nice to write down things in full, but it also renders the discussion more complicated than it might otherwise be...
I'll quote some of the features you listed, making a few comments.
Again, this is not a criticism. I hope these remarks may be of use in rationalising the rules.
I'll use these acronyms: H=hard; S=soft; HNV=hard non-velar; HV= hard velar [i.e., k,g,ch]; PS=phonetic ["true"] soft; HS=historical soft
Adjectives in the male and neuter locative singular take "-ym"/"-im"-ending.
FEMALE-SPECIFIC DECLENSIONS ("-Y"/"-I"-ENDING):
The alternation i/y is regular and always present: HNV and HS want -y, HV and PS want -i.
This means that in Polish the sounds (say) ń+y, c+i cannot occur, ever. It's always ń+i, c+y (and so on).
SNA: sosna -> sośnie [sna -> śnie]
This kind of behaviour, and similar ones like miasto->mieście, are necessary to respect the Polish phonotactic rule which says consonants in the same sillable must be all soft or all hard.
Softening of the final n to ń induces the softening of the preceding consonant to respect the rule... there's really no other possibility...
Ę: zwierzę -> zwierzęciu [ę -> ęciu]
IĘ: imię -> imieniu [ię -> ieniu]
UM*: muzeum -> muzeum [um -> um] (no change)
Neuter nouns ending in ę (and often referring to the young of animals etc.) acquire a further syllable in all cases different from nominative. Latin names in -um are invariable in the singular. So there's no irregularity of any kind here.
Nouns ending in Ć, Ń, Ś and - have their respective final letter lose their
accent and have "-iach" attached at the end, e.g. ćwierć -> ćwierciach
Of course this a general orthographic rule: the sound ć+vowel is spelled ci+vowel, always.
I won't comment here on the vowel alternation but them too are (to an extent) predictable: e.g. ó in closed syllables, o in open syllables; e.g. take gwóźdź->gwoździu (nail). The nominative is a single-syllable word and hence a closed syllable. The locative is gwo-ździu: open syllable and alternation to o. The same occurs e.g. in the genitive sing. (Kraków->Krakowa), genitive pl. (słowo->słów) etc.
If it is possible to assume that general phototactic/orthographic rules like the ones above have been acquired, the locative case rules can be stated in a much more compact way:
MASC,NEU, FEMM -HNV => '-e
MASC,NEU -HV or -S => -u
FEMM, -HV => '-e
FEMM, -S => -i/-y
Where the apostrophe ' indicates softening/vowel alternation (if relevant). The rest are details :)
Anyway, congratulations again on the job you've done :-)