although you will probably end up with a good performing waterblock, i dont know why you are trying to fit your design around those heatsinks.
there are a few problems with them, the main one being that they are made out of aluminum so they will not perform as well. i will suggest a better and easier idea:
make similar heastinks out of copper, they seam quite easy to make with a lathe or even attaching copper to a drill and spinning it while making the groves with a file, infact i may try somehting like that...
this idea also makes it easier to attach it to a base and sides because it can be soldered easier, you can also use an end cap to encapsulate it.
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