Depending on how consistent the changes are I would make the first pass with the “Transliteration using SIL Converters” project type. You can use a cc table or tec map to convert the orthography and major vocabulary.
Someone else will have to speak to the significant differences between Interlinear and Adapt-it. Both tools can use the Paratext files and produce output for Paratext so in some ways it would be a matter of preference and whether or not you want to learn a new tool.