What sort of wheel are you using? My boy started using his wheel from the day I brought him home at 7 weeks old. Perhaps others can make suggestions on how to lower it a bit so yours can climb into it easier.
Also, every time I took him out of the cage, I'd gently place him into his litterbox and wait till he uses it before I let him out. I usually do that for about 2-3 minutes, where I'll gently put him back in again if he walks out, and he got the hint quickly to go first and then he can leave. But then again, I've always been really lucky, as he was very easy to litter train... Actually, he never needed training, he just knew.
You say that you have fleece and towels in the cage.... Be careful with the towels, because if he starts digging through the towels, his little nails can get caught in the loops and could end up pulling a nail out. Safest to stick only with fleece in the cage. I only use a towel after baths, when he is supervised.