This probably isn't the solution to your problem, but speaking of vacuum line issues there is a design flaw in the PCV system. The rubber elbow coming out of the intake just behind the throttle body will slowly destroy itself over time. I replaced mine at around 100k and it had almost split in half. You can get a replacement from the HELP section at any auto parts store, just get the Ford diesel truck one, the one that's the same at both ends, and borrow their hose cutter to match it to size. It's like 8 bucks.
Improvement in performance isn't really obvious, but it's nice to not have a hole in your PCV system that could manifest itself later as a bigger issue.
Also if you have your original fuel pump I would test the fuel pressure, that's what ended up being my problem when I had issues similar to this.
edit: I continued browsing the forums and found a topic on this issue, sorry to bring it up again, I had not seen anyone else mention it before!
Last edited by C_Red90; 03-13-2016 at 06:39 PM.