The land-animation effect lasts indefinitely. It doesn't wear off during the cleanup step or when you lose control of Waker of the Wilds.

If the ability targets a land that's already a creature, that land creature's base power and toughness will become 0/0, overwriting its previous base power and toughness. Other effects that modify its power and/or toughness (including any +1/+1 counters that were on it) will continue to apply.