Id pick him up as the books advise Kim, I do think that the scruff of the neck pick up is ok as it reminds them of the mother and the way she picks them up but I'm not too hot on the shaking. (Little brain getting bumped about, but that's just my take on it). If you hold him that way and make eye contact till he looks away. You are letting him know who's in charge. It has to do with the dominant Dog they tell me (Alpha and all that) Make sure you do it till he looks away though and repeat the process till he gets the message. Then he may pay attention if you say NO! My Pup Harry responded to this well.
Sounds like a handful but Im sure he will turn out just fine cause he's loved:>)
Good Luck with the training.
A