I know the quality isn't the best, but from what I gathered, it seems to be pretty cool. I recognized the first two sections from one of those clips you shared earlier.
As for critiquing what you have so far, here are my thoughts (if they mean anything):
Seems like you have some kind of structure/progression planned out, which makes things a lot easier. Just remember that the guitar doesn't have to fill up everything. Having some breathing room will really make it much more lively and energetic. I know you have the skills and technique to play some really busy lines (hell, if I could play like that I would be doing it too), but remember to keep that under control. Quite often the best line/riff can be the simplest ones.
Someone earlier mentioned adding odd rhythms. While I think this is a really cool thing that most bands don't do, I'd advise you to really think about it before employing it. Nothing's worse than a section of a song that you can tell is just there to be "technical." It sounds out of place, and that really ruins the mood created by an otherwise well written song. But if you're up for it, definitely give it a try. You can have stuff like the guitar playing a passage in 5/4, whereas the rhythm section is playing in 4/4. After 4 repetitions of your guitar part (and 5 repetitions of the rhythm part), both can come together to create a really heavy and intense jam in 4/4 (or whatever else you want). That kind of stuff, in my opinion is really cool. In one of my new band's songs, we had a section where all of us are playing the same little riff that's in 7/8, then halfway through I switch into a simple 8/8 part (I play bass, btw), and then we come back together into the "chorus" of the song, which is in 4/4. It serves as a really effective resolution, because the earlier part is so chaotic.
Another area I think you should look into would be your transitions into different sections. I totally understand that you're pretty much forced to "fade" into the next section, and you probably have some thoughts about how to go about doing it on a real recording or band setting, but in case you haven't thought about it, here are some suggestions: you could do short repetitive clean/acoustic arpeggio fills, and then bust into the next heavy section. Opeth likes to do that, which I'm sure you've noticed. Or you could do kind of the opposite, where you go directly into say riff #3 from riff #2 (i'm just using these as examples). These really work when you want to avoid excessive breaks for fills and stuff like that. Plus when using this "technique" you can emphasize the change/shift into the new section by totally changing your rhythm around. For example, in riff #2, the drums could be a fast double bass and snare type, but then when you go into riff #3, it could be much more of a groove with a consistent cymbal/hi hat attack keeping the rhythm/tempo going.
As for your tone, I believe it too needs some work. The first thing you have to remember is that a good tone when you're playing alone will probably suck when being recorded or playing with a band. This isn't always the case, but more than likely (especially with heavy distortion), it'll be true for you. When recording, I'd advise turning your bass down. Somebody said to turn bass to 10... I completely disagree with this. You want to cut the bass because the guitar occupies the mid range of the sonic spectrum. Addin excessive bass on guitar will bring in so much mud, especially when you layer guitars and then add bass. As a very general guidline, I'd keep my settings around say bass: 3 or 4, mid: 6, treble: 5 or 6, depending on preference. Remember that cutting on the EQ is better than boosting because usually when you jack up one of the frequencies, you're very likely to get a muddy sound. Your playing technique matters a whole lot more when recording too. Try to get a better sound by first adjusting your hand positioning (eg. closer to the bridge), then your guitar tone knobs, and finally your amp EQ.
Hopefully this has made sense. If you have any questions, feel free to ask.
Aborted Fetus