The two ferries serve two different sets of priorities: slow/nostalgic/northerly/cheap, or fast/modern/southerly/pricy. If your itinerary creates a need to cross the lake in two different places, or you’re just curious to try out both boats, then this approach makes sense.
As for House On The Rock, Roadside America has a great write-up about it.
Actually, Milwaukee is 99% sure. I did mention we’re thinking about taking the fast ferry to Milwaukee, doing some sort of a loop, and taking the Badger ferry back.
The big question is how far north and especially how far west we’ll be going. We have to do some mileage math and figure out what and how much we want to see. I’m thinking either we keep it easy and manageable and stick to a Milwaukee/Madison/Door County triangle, or get ambitious and also make it up to the Apostle/Madeline Islands.
So much to see and do in Wisconsin. We’ll definitely have to make more than one trip! If we didn’t have the kids with us and it was my call I would head straight for House on the Rock, then due north and spend the rest of the week kayaking around the Apostles (taking mostly state roads instead of interstates for driving scenery, and picking up some good sharp cheddar along the way). Anybody want to room & board two boys for a week this summer? 
Near Racine there is the Jelly Belly factory. Not really a tourist destination, but an interesting stop. You can buy misshapen Jelly Bellys called Belly Flops for cheap in a 3lb bag. Bought ten bags while there, lasted about the months.
As mentioned, Door County is a must (Al Johnson’s!). I also recommend Cave of the Mounds for the kids, which, coincidentally, is not too far from House on the Rock! Lambeau Field is really special. I get choked up every time I walk inside.
GO PACK GO! 
Might want to check in on this one before making the trip. They say they will stay open this summer but you can never be sure… BTW, Solost, there are other great outlets in and near Pleasant Prairie, if that’s your thing.