The hole you punched may just be too large. Playing with filters is a very delicate task. You may want to get a set of the MAKE filters and play with it.
Finals tutorial for MAKE3 summarizes the relative effects very well:
1. Effect of filter on the sound bore; less dense filter = more treble, less bass; more dense filter = less mids.
2. Effect of filter on the air hole (or behind the driver if you have access to that). The effect demonstrated here is very marginal because you really want to tape it up if you want to reduce air flow. No filters are dense enough.
3. Effect of foam in the sound bore, easy to understand. It is similar to how we used to add foam cushion on earbuds
Did you try playing with eartips? Anyway, if you find yourself spending too much time on E3000 but not on the music, then they might just not be right earphones for you...