Tool fan needs help with speakers (and electronics)

I'd suggest putting more $$ away until the next album, then you can go wild on a much more expense system.  Ahem!!

But seriously...I have a pair of NHT 2.9 from 1999 that I got a great deal on for $1500/pair (didn't need the 3's), just changing the electronics over the years because I just loved the 2.9 for rock/metal/trance/psytrance etc...So the above that mentioned the NHT's gets my thumbs up considering your budget.

I'd also recommend a great headphone DAC/AMP + headphones...Tool in the cans is another dimension for listening and the way the industry is going, the quality of that sector of gear is amazing for the $$.

Tool, Alice in Chains, and Clutch are what I play most often. I also like some old country, some Hank 3 and some more extreme metal.
I will get flamed for bringing up Tekton but especially for the kind of music you like..... Tekton DI used and maybe something like a Parasound hint used would give you a kick ass system around 4kish. 
Also agree with some other posters in that room at minimum you will want to get a big area rug and some mild wall treatments. 

Another brand I've always been curious about but that makes huge speakers that will fill a big room is Tyler.  I assume they're not the last word in refinement but I don't have direct experience.  They sure look fun.

http://www.tyleracoustics.com/Deal%20of%20the%20week.html