You can change to genetic regardless of what level your homun is. You can also remake the homun as a genetic without penalty (other than having to level the remade homun, of course).
Once it's 99 and evolved, and you're a genetic, you can (and should immediately) take it to the npc in lhz and change it to homun S.
The thing you need to be really careful about is if your homun IS level 99 when you change to genetic. As soon as you change to genetic, the level cap on the homun increases to 150. You can thus level the homun past 99 before changing it to homun S - this is BAD BAD BAD because the stat growth as pre-S homun is much worse than as homun S, and you permanently miss out on hp/sp and stats if you level if past 99 before changing to homun s. Just like players, homuns can get overflow exp - and you can't see the exp bar to know whether this is the case until you change (if you change and see no homun exp bar, that means it will level on the next kill); it is thus quite easy to end up with a 99 homun with enough exp to immediately level to 100 if it kills anything (even a poring or herb plant) once you change to genetic. If your homun is 99 when you change to gen, you need to be extremely careful until you change it to homun S.
