A month will be longer than your other trips. I look forward to you posting about it. The routes you propose will be across islands. I read some rental companies don't allow that, but I have no experience. Or are you just going to rent a new one on each island? A video of you traveling with a bike by ferry would be interesting though.
I have watched one couple that did a motorcycle tour through Flores. I believe the place to rent is Labuan Bajo, I have not found any reliable advertisements for sewa motor across Flores although there may be a way once you have boots on the ground. The other place I have read, but it did not seem reliable was Maumere. The last travel article I read about it, they were 50,000 a day, but it was from 2014. Wikitravel says they are 75,000 now. I assume you could get a diskon for a long term rental.
In full disclosure, I am a little jealous. I have been plotting the same for a few months, but have been a bit short on funds. You will probably beat me to it. I wanted to do a tour of Flores by motorcycle and then to Kupang to tour Timor. If I had 30 days to blow, I would also make a trip to Timor Timur too. I read that tourism to the country is less than 13,000 visitors a year. It would seem to fit with your spirit of travel, but you need to secure a visa ahead of time of crossing by land.
Some of the advertisements for motorcycle rental from Manado have been less than reliable and the rates much higher. The most consistent advertised one was 350,000 idr a day. There are a lot of expats on the forum from that area, so you should be able to get a lot of support and possible meet more westerners on that trip. Also, the infrastructure for tourism and travel is much higher in Sulawesi than Flores.
My only advice is not to over plan and work in some downtime. From your Kalimantan and Java trips you had a few delays.