1) the fuel pump relay mod/bypass - no negatives, but theoretically it may shorten pump life (I did it to mine on my JSpec swap because my old relay, while working was severely rusty)
2) One mentioned on Team3S - not sure it works but I did it anyway: To improve the feel of your stock brake lines/simulate the feel of stainless lines - use zip ties around the stock brake lines every inch. Supposedly will help limit the expansion of the lines? I tried it, but I didn't have a real feel for how my car felt beforehand - it had been so long on the stands and I only had about about 100 miles before the swap.
You can remove the resonator from the intake. It takes about 5 - 10 minutes depending on how handy you are.
Unscrew the clamps on the intake piping and take out the resonator from underneath. Then just plug the hole using a freezer plug (available at any auto parts store) or any type of bottle cap that will fit the hole tightly. Then just put the intake back on and you're set.
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