The low treble spike won't get better, no matter the source or 'burn-in' hours. They have it and we have to live with it. I simply use a touch of eq and love the result. Regarding the bass, I also find them a bit 'light' especially in the first octave, that's why I like to add a low shelf on the aforementioned eq, to compensate for that.
Lately I find myself using the 'HF boost' filter in conjunction with the Comply tips and I think I like this combo more than the 'Reference' filter + stock tips.