Hey, just to let you know....
Replacing the fuel filter (and pump) has given my car a boost during gear changes. There was a nearly un-noticeable delay when accelerating again after clutching. The new filter and pump has helped a lot.
This morning was 37F, and it still sounded a little weird (maybe need to check the things you replaced, I already did the cps) but overall a lot quieter and smoother on a cold start.
Hope you're having good times w/ your e46.