V6 3 speed manual

Stay with the hydraulic linkage that came in the Dakota. It makes life exponentially easier. It’s been a while, I can’t remember if the 3.9 is an internal balance, but it seems like it had extra material on one side of the flywheel on account of balance/firing order. I’ll have to double check for you. Manifolds will make your life simpler for sure. Are you just putting a big two barrel on the stock manifold?