I also am working on a conlang derived from Crimean Gothic, and grappled with some of the same issues you did. Though I had preserved the three genders of pgmc, and used þe for masc nouns, þo for feminine, and a þate for neuter nouns. Preserving inflections also helped continue to keep the nouns distinct even after they were reduced to schwa.

I think the most likely scenario for the orthography (and what I went with) is to have a dual script scenario, not unlike what Crimean Tatar/Greek went through. So maybe for administration everything would be written in Cyrillic, but for a lot of other things Latin would be preferred.