As far as I know, silica should not have any noticeable taste.
I'd suspect the DIY wick material. Boiling it should not hurt, but may not be effective in removing manufacturing impurities, either. Some recommend torching silica, as well, but I've never seen a need to. I'd try a different source, if I were pretty sure that the silica wick is the problem.
A concern that I have with what I read above is that you seem to be using a bigger wick (thus bigger coil) than stock ones, with no 'flavor wick' on top. I would think that the 3mm wick may get pinched too much when putting the top cap back on, reducing it's effectiveness in wicking.
I'd also be concerned with the coil shorting to the top cap, as I suspect that the 'flavor wicks' are really there to prevent direct contact of the coil to the top cap. I noticed that this is very possible on my first eVod rebuild, when I used a 1.25 x 2.5mm (approx.) oval coil. I'd imagine that a partially shorted coil may cause what you describe.