Firstly the misshapen baits, you're likely boiling on too fast a boil. It only needs to be on a light simmer. I do 14mm baits for 3 mins on a light simmer and it never damages them.
Secondly the smell, it will wash out on cooking, maybe more so if I am correct with the above issue. (Too high and it also knocks out the dye a bit too FYI). 10ml per 1 egg is all I use and I can get it coming through after 24hrs in the lake still. I air dry for a week, put them in a bag, coat them with flavour, air dry again for a week and repeat once more. I'll then pot them up and add a couple sprays of flavour (or mix of flavours) and give them a shake. A few days and it should be absorbed and you'll have very over flavoured and smelly baits. It soon washes out to a good level though.
Also remember some flavours will linger more than others, and quality will vary. I have found catchitlabs, AA baits and some of the CCMoore flavours to be good quality. Sometimes it's a bit hit and miss but if you can get samples sent out then it saves on buying a big batch of dud flavour.