The problem with the flute is the part / sequencing more than the sample. There's no pause for breath, and the sequencing is really kind of mechanical. It's hitting a bunch of equally-powered notes without a pause for breath.
At 0:34, the kick is muffled. That's a good kind of bassy hit to have, but you also need to have the higher frequency in the kick -- give it a small bit of click to go along with the oomph. That'll make it easier to hear and also give it some definition.
The break at 1:21 is awesome! I like the glitching.
At 1:36 you can hear how muffled the kick is. When you add that click, you should also raise the volume until it sounds fitting. At 2:07 to 2:53 it sounds like you don't even HAVE a kick. You gotta get that level figured out. Too much subby oomph, not enough click, and volume too low.
I've used Slate Drums and they aren't as customizable as other libraries, but that is not so much an issue for what you are experiencing as far as I know. What I think might be the issue is that your "room mic" is too high, and the regular volume is too low. This gives it too much of a roomy sound and not enough of the core sample's volume. So in general your drums are not hitting with as much power as they should, and as much power as I know the Slate drums usually have... So fiddle with the room settings and raise the volume on everything! But don't go overboard then have people blaming me because your song is all drum and you can't hear anything else, there's a good range to be in without going overboard, right now I'd say you are under.
You said you're working on a new version, let me know when you have it up and I'll try to comment on it faster... sorry.
P.S. Don't try to "meld" the guitars and bass, they should sound distinct from each other, while being EQ'd apart so that they don't bleed into each other. If they're just kind of bleeding into each other, try a 200hz low shelf cut of like -1db or more depending on how much bleeding, cut the bass at your kickdrum's bass frequency and between 250hz-600hz or so, that low frequency area of bass guitars that aren't worth crap. 800Hz should be your "body" type area of the bass with that good buzz, 0hz to 60hz or so is your sub bass which you should either leave as is, boost, or cut depending on how much bass you want. BUT If you can't hear this, I'd be careful... you need to be using a system that can reproduce the sub bass accurately or you're gonna have a mess in some peoples' systems. I'll usually high pass a bass to about 2Khz but you can also boost it a bit at 2KHz for more nice buzzy pick sound. I mean, you don't have to highpass to 2KHz and I know there's more high end frequencies that are awesome, but unless you're making something like "
" you don't really need those freqs.