The is no direct anything from Windhoek to Maun other than Air Namibia.
The way to get via bus is catching the Bus that runs from Windhoek to Gabs, After crossing the border, you hitch hike to Ghanzi, and then catch the bus that goes from Gabs to Maun via Ghanzi.
If that seems too much of an effort. Go all the way to Gabs, then catch the Maun bus from there.
Best way is to stay at the backpackers and try and catch a ride with people who are going this way.
There are small local buses but I have lost the contact numbers. They run from Windhoek to Zimbabwe and pass through Maun. Last I heard they were around 400 rand to get to Maun.
If I was you, I would head via Maun first. The hiring in Namibia kicks off towards the start of the year, while Maun is towards the end of the year.