Well, being a fan of music, naturally, I regard TOOL as one of the greatest bands of all time. In my opinion, the only time to cover a song is if you can make it better or dramatically different and still of comparable quality. I almost didn't want to listen to this because I didn't want to have anything else associated with this song in my head.
With that said, this is a good song. If I had never heard the original before this, I would be very impressed. As far as recommendations, I would just make many small nitpicks over various vocal instances in the song, but you've got your style and we'll leave that at that for now.
The acoustic element's not bad. Granted, with no budget, there would be alot of great guitar tones and recording techniques to put to use with a cover like this, but that's not the case. The breakdown/solo section sounds pretty cool. The fast playing before the final chorus is one of the main examples of losing that key energy you get from distorted guitars.
So being in the very early aspects of technical knowledge, myself, I can only really suggest singing quieter and more melodic since it is an acoustic track. The vocals sound more geared towards a full-band performance with heavy guitars. I'm just suggesting more gentle, not dramatically quieter. Or you could just go the full route and add distorted guitar and have no limits.