What a task! And I thought I was the only crazy wagon boat hauler....
What is the beam on the boat? It may be so wide that when you put it on top of the car it will cover it like a hat....
Here is the most I've gotten out of my rack -

That is a Yakima Load Warror with extension on factory bars. I estimate the total weight to be about 140 pounds (2 12 foot kayaks - 45lbs each + cargo box with kayak saddles ~ 50lbs). This is exceeding the OEM luggage rack rating by 40 pounds.
What you have to be careful with when looking at aftermarket racks, is a problem with a short distance between the cross bars. The OEM rack allows you to spread the bars almost over the lenght of the roof. When you get a Thule/Yakima one, you will mount your towers in the door jambs which limits the spread. You may get a greater weight rating (maybe 150 versus the 100 oem) but you will not be able to spread your bars enough to support the load.
To avoid this, I would look at the aftermarket options that mount to your existing bars. I would also get a bunch of foam blocks to further spread the weight throughout the roof. Your idea of the 2x4s may be a good one too. The goal would be to spread the weight out as much as possible. I don't even want to start with the securing of the boat.
With that said, I would not do it unless I could stay under 30 mph.... And I don't say things like that a often....