Lens alignment

I often see two opposite cases in lens repair: the optics are in perfect condition, but something prevents the lens from working (broken autofocus, falling apart enclosure, and so on), or - everything seems to work, but the optics are in a terrible state. Today - about the second case. The Sony FE 24-105mm G OSS lens was fully submerged in some body of water, dried out, and remained functional (the aperture, stabilizer and focus all still work), but with awful stains everywhere. I'm facing a