It can't be anything to do with the lowering links (longer dog bones) as the shock position is related only to the triangulation of it's top mount, bottom mount and the linkage's engine mount. If you take the linkage bones off completely, the shock will still be in exactly the same position at full extension as it would be with them fitted. Full extension is limited by the internal bump stops built into the shock.

The only thing that would bring the shock spring closer to the rear of the engine at full extension is if the shock's free length was too long. Have they sent you the right length shock?

__________________