Impossible to answer without context. The second sentence could mean that your son wakes you up 'most often', implying that at other times he wakes up someone else (eg. his other parent). 'Sometimes my son wakes my husband, but he wakes me up most often'. But perhaps you mean that being woken by your son occurs more often that being woken by something else - e.g. an alarm clock?

I would suggest that you substitute "usually" for "most often." But usually my son wakes me up.

Depends on the context. The first might contrast with some other event...you continue sleeping. The second might refer to the fact that someone else might wake you (less often). I hope that is clear.... ;-)

very little difference

Sorry, more context here. My alarm clock usually rings at 8 o’clock. But (most often) my son wakes me up (most often).