It's your call. You expressed concern, asked a question, and I'm just giving advise. If I made a change, and that change seemed to cause an unsatisfactory result, I would undo said change to verify it "it" was indeed the problem.
In this case, it's just swapping some vacuum lines around so there is no real time lost. If the car still acts up, you have another issue. If the problem goes away, you need to figure out why it's causing the issue in the first place. Intermittent stumbling above 4K is not a typical result of doing this. Once you figure out why it's happening, you can enjoy the mod to its fullest.
If you are at 45K on the stock plugs you may want to pull them out, and regap them or replace them with new ones. With that kind of mileage there could easily be enough wear to warrant removing them, and with the same effort involved in either regapping stock plug or replacing, I'd say replacing is the safer bet. Most guys here gap new plugs to .028" I believe. I gap them even lower, but I run more boost than most people here so it's warranted.