Temp difference in water between blocks is like 0.2c. Route them whatever way gives you less bends and less tubing (less resistance), order does not matter.
As for the Y choking? The Y he listed is ideal. Barbs on the MCP350s are 3/8" You dont have much choice. There was mention of how to mount them though, IE ontop of each other or something. I didnt really read it but I think it made a difference in either ease of usability or actual performance. Stacking them on top of each other and having that Y as close to the inlets as possible makes sense though =)
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