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Manual clutch linkage, Borgeson all fit fine. Slight interference with manifold shield and reverse lockout linkage bracket easily rectified with a little grinding.
I am using the C6 manifolds that are on a lot of LS3 crate engines - the short ones with O2 in the center. I use a batwing oil pan, Jeep steering box, and modern 6 speed. No shift or clutch linkage to worry about, and no problems for me. Many here use the C5 manifolds as well. Just be sure you don't have the GTO manifolds that come on some crate engines - they flare out too wide.
Your engine mount adapters do make a difference, because the engine location can be forward or back from "stock" depending on the mount you use.