I’ve never used a clone-a-willy kit but my father was a beekeeper and we used to use moulds for making beeswax candles to sell during better times. I can remember the owl mould being notorious for air bubbles.
@JGood is absolutely right, you need to shake the air bubbles out (I was wondering about using a corded wand against the mould but that’s coming from the woman who infamously used the butt of her cordless wand as a hammer 
). My other thought would be to tilt the mould slightly ans kind of pour the silicone down the side of the mouls, slowly uprighting it as it fills. Again though, you’ll want to tap it a few times to be sure.
Unfortunately foe your existing bobbly knob, I think it’s probably too late. It’s at least a talking point and a practice piece!
@Phil44 how about attaching a moulded willy of your penis to a broom handle? That way you can enjoy filling her without worrying about your mobility. A fucking machine is always another possibility but they’re not cheap.