Have a look here at our taming tips guide
http://www.hamstercentral.com/wiki/Taming_tips
I think that as you have a little one you should definitly start to wake him up at suitable times and the guide gives details on this. He sounds like he is making progress already and it is early days yet so he will still be nervous and unsure until he settles. You can also try getting him out into a ball or box and then getting in a dry bath with him and letting him walk all over you. Pick him up and lay him down a lot during his exploring so he gets used to being lifted. The key is to master the hand to hand running as then they can feel your hands all around them and the quickly gain confidence. Get you little girl to do the foot to foot paddock with you as detailed in the guide and she can then lift him back in if he tries to get over the legs!
I am sure he will be tame soon so be confident and you should do some taming when she is not there to progress things quicker. It is no hardship to wake a hammy up as they can always go back to bed. I would suggest you use an easy to get at house such as an igloo with no bottom so when you want to wake him you can just lift it up. The get very scared if you are detaching house roofs or poking them out of small boxes and respond much better to just being uncovered.