Your on the right road now.
If you want to modify the induction system you need to take the kink out of the hose so the rest of the system can breath first. You can either do a new intake manifold. I think the runners on the TFS series are a little large for a stock headed application. You would still pick up power, but probally loose some torque. The Cobra/GT40/Explorer would be cloerer suited. Really, I would look into a TMOSS intake. He ports the lower (the upper actually flows really well) so it matches the upper, which will be more then enough for your stock heads, plus you won't loose any bottom end. I'm going to send him my lower intake of my performer to match the TFS heads I have.