Definitely wait until it stops - more precisely, wait until fermentation stops. Yes, check gravity, and then wait three or so days and check it again. If it's stable, then bottle. Ignore the bubbling - it really doesn't tell you anything. The only way to know if it's done is to use the gravity readings.
Sometimes the instructions are useful, more often than not, they're crap. Sounds like the instructions that came with your kit are not so good. Just ignore the timing schedule in the instructions. THe beer is ready when it's ready, not when the instructions say.