I think they do take a while to come round after being woken
Our last hamster needed five minutes or so after waking to be fully with it! It sounds like you're making progress and it will probably be easier when he feels more confident with you both - gets used to your presence and scents. Have you done the tissue trick? You put some sheets of toilet paper up your sleeve or down your bra against your skin and leave them there for a couple of hours. Then tear the sheets into strips and put them in the cage for him to take for nesting material. You could both do it.
I would avoid spot cleaning much if possible - the Barney is a big cage so shouldn't need much doing for a while. Is he using his potty? If he tips it up again just add a bit more sand to it but leave the tipped out sand rather than spot cleaning.
I've found they poop a lot when out of the cage at first and think it's an anxiety thing and/or a younger hamster thing - our older ones have better control!. The poops aren't dirty really though - like little hard seeds.