That equipment list looks very good. Four Funkywaves 18.0s! That will be an incredibly high quality bass system. Make sure you select the TC sounds LMS5400 Ultra drivers when you talk to Nathan.
As for the Yamaha, it will make a very nice preprocessor, but its a shame much of what you are paying for in that unit will be wasted, since it has such a robust amplifier section. You should check if Yamaha has a pre-pro only version of that AVR. Or, when you hook up your speakers, compare the Yamaha to whatever amp you end up with- you may find that you won't need the external amplifier at all if it sounds exactly the same. Quite honestly, it shouldn't sound any different, the only difference there should be is a 300 watt per channel amp will get about 3 db louder, which isn't much. It might be heretical to get such nice speakers and power them with a Yamaha AVR, but in theory there won't be any difference aside from a slight amount of output headroom.
As for the Lexican vs ATI brand, get the ATI amp, that was a good catch by Granteed.
For the PC, the list looks very good. For all-out performance disregarding price totally, I would skip the WD disk drives and get a couple of
these, but that would make the PC hilariously expensive, but also insanely fast. Like I said before though, I wouldn't try to use the PC as the source for blu-ray playback. I tried it, I didn't like the inconvenience, and also I was never able to get the picture to look as good as my blu-ray player did. One thing which will help you a lot is a all-region blu-ray player, so you can playback hollywood movies just as easily as Indian movies. In order to do that with a PC, you have to have a hack with the major blu-ray playback software that I know about (Cyberlink and Arcsoft).