Hey adam, good plan, bin the factory manifold and forget about CT20/26 turbos, you'll be much happier with the Garrett. THough I think you'll find that a 2560 is a T2x flange, not T3.
Merits of merging particular runners has more relevance with a split-pulse turbo exhaust housing, in your case make the manifold runner order to suit the layout of your engine bay and turbo placement, and focus rather on a nice narrow angle for the runners to meet at the collector.
Either 1" or 1 1/4" steam pipe will be fine, in theory the 1" will keep gas velocities higher (potentially better response) and should also have the flow potential for anything the 2560 turbo can provide. Of course you'd have to do a bit more work transitioning to the smaller 1" pipe though from the ports in the head.
Cheers
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