Im no expert but this is how i'll do it , if were in the same situation, collect all your custom changes from db,conf/import, official NPC (if any) and all your custom scripts, in source, collect and save all your modification snippets,
download rAthena head revision, and apply the needed change,
also try to translate the code from eAthena to rAthena ( e.g. skilllv (ea) -> skill_lv (ra) )
yes this is tedious work but you'll finish it eventually, hope someone with better solution shares..