1. Most games will not be able to fully utilize a quad core for a while as game engines are coded to scale off 2 or 4 threads, while Hyper Threading is great for some productivity software, the gaming industry is more or less ignoring the existence of 8 thread machines because they need to sell a lot of units, and very few have those at their disposal. So I would say no, it's not worth the extra bit of cash.
2. The RAM as I said before is overpriced, and the heat spreaders will interfere with almost any cooler around. 16 GB is also quite a bit too much for a gaming rig, even 4 GB would be sufficient if you didn't run anything on the side, 8 GB will be plenty. As for RAM, the frequencies and timings do make differences in benchmarks, but for the most part with modern systems they operate so fast no matter what that you won't really notice the difference between them unless you're doing something insanely memory intensive. This
Patriot Gamer 2 8 GB set for $37 AR will be fine for your system.
3. The 660 Ti will not affect the prices of its bigger brothers as it of the same generation and not meant to compete with them in any way. The 660 Ti will likely cause a drop in the price of the 560 Ti and possibly the 7850 depending on what price it launches at.
The numbers for most SSDs in terms of max read/write throughput is usually done in the most perfect circumstances that the manufacturer can come up with. I don't quite remember which SSD it was but around a year ago there was a drive boasting the highest throughput of any SSD on the market (I think it was an earlier SF controller) but when it came to certain tests in Anandtech's tests it fell flat on its face with speeds barely matching mechanical drives (like random writes).
As both drives utilize Marvell controllers I don't see much issue with either though, personally I can recommend the M4 as a great drive. According to
Anandtech's benchmarks the Plextor is indeed better in almost every way, and as it utilizes the same controller the reliability aspect is likely close to the same unless they've botched their firmware somehow. At the end of the day though, both drives will handle your data so fast that they'll both seem of roughly the same speed so I'd suggest going with whichever you can get cheaper.
According to
AT benchmarks either card will be able to handle BF3 with the 670 edging out a bit. Overall the 7970 GHz edition seems to average out better, but either card will be able to handle almost any game you can throw at it.
Edit: I'd also like to once again add that I still don't see how this build is coming out to be so expensive, as others have stated spending more on computer hardware isn't always better. Your system costs more than twice
mfenn's mid-range system build but will only edge out in performance a tiny bit. With a single GTX 670, not the crazy 690 you're looking for, you can play any modern title even at 2560x1600. If you want EVERY modern title at highest settings possible then look into 670 SLI or 7970 GHz CF set-ups, both cost less than a single 690 and will likely outperform it in most circumstances.
Why are you aiming for 2 256 GB SSD's? If you need storage space SSD's are still nowhere near the cost efficiency of mechanical drives, just pick up a single 128 or 256 GB SSD and a 1 TB + mechanical drive to use as storage for non-essential/commonly used programs.