Might be hard to offer advice without a seeing a video of you but here goes nothing...
It sounds like your way of learning 3's is right on, trying it off small side hits and such.
Going off bigger jumps requires you to pop off the lip more than you would a side-hit. Don't just try to carve off the lip into the 3. From your description I'm not sure if this is your problem or not, but had to mention it anyways.
If you're spinning frontside, try to grab Indy. What this does is let your upper body (and specifically your right shoulder, if you're riding regular) to drop down, which will naturally let your body move forward and even out your spin in the air. Grabbing may sound like it complicates the maneuver but it doesn't, not really. Suck up those knees.
Like longboard said, practice a bunch of straight airs off the jump until you are absolutely 100% certain you can clear the knuckle and land in the "sweet spot" every time. How fast are you going when you straight air the jump clean? Note this, and then when you're ready for a 3, go just as fast, and then a little bit faster. You're gonna scrub a bit of speed when you start entering the rotation off the jump so going just a little bit faster than your straight airs will let you clear the knuckle.
Finally, more of a question, are you speed checking a lot before the jump? If you are, this will prevent you from coming off the jump even and controlled. You should ideally be making only one set up turn before popping off your heels.
Let me know if you got any more questions. I love a good frontside 3.