Maybe the path of least resistance is to go the opposite route. Instead of adding urgency and punishments, get rid of it. Make it so we can talk to our companions and we all come to realize the ceremorphosis isn't taking place sooner in the story. What if we come to realize we've been on the ship a few days from the time we are infected with the tadpole to the time we manage to escape. When we are meeting our companions, those like Gale and Lae'zel can mention how it's odd we aren't turning already, and something is definitely off about the situation. Maybe even add a line from Gale about how he would like to of course get the tadpole out as soon as possible, but we don't seem to be in any danger of actually turning. The goal of this being to give hints to the player that they don't need to rush. Make the companions encourage the player to long rest, not yell at them for it (especially the first time you decide to rest). Hell, to add to this, give more dialog barks from the companions wanting to rest for the day. Give companions who have no features or spells left the eyelash icon from the original Baldur's Gate series. A visual reminder that the characters need to rest.
