Wow, with a budget like that, this thread has created some excitement.
Some other things to consider that I have not seen mentioned:
I have heard the afar home for music and it simply sounds amazing. It also looks amazing like a piece of art almost.
The Ultra is also a beautiful sub, though I have not heard it. At its pricepoint as has been mentioned though there are far better choices.
I have dual Captivator 1000's and think that Jeff (Owner of JTR) is a stand up guy that designs and builds some truly amazing performing speakers at a great value.
They definitely do not have the finish that a fathom does, but they are every bit as good on music and truly outperform it by a great margin for HT. The caps look plenty good for me, but thought it was worth mentioning that their appearance is definitely more along the industrial look.
From a fellow 49er fan for over 30 years I would buy a submersive HP or dual S1's or an S2 from JTR and don't look back or worry about the value that you will receive.