I can't say if this is the best method. It could be fine or having more contact with the board mask overall may still provide quite a bit more heat transfer. Even though the board is not a great conductor there is a lot of surface area that is lost by using raised pads. Before committing to a large purchase I'd suggest testing both ways to see the temperature difference.
I'm still working on getting bitcoin into $$. FC4B has nothing until Tuesday now.
How many bytes of data to you have to shift into each Avalon chain to configure the chips?
That would be 84 same for both banks + 32 different = 116 bytes.
At 4Mbps that's 29uS, though I think it will take a bit longer due to software clocking limits.
edit: oops. That's bytes not bits. x8 = 232 uS.