The second case I linked is what I use for my current setup. I love this case. It has good cable management and lots of fans slots for good airflow. Honestly, this is a hard one to recommend though as we all have our own preferences for how a case looks. I've always had good quality cases from Antec and Cooler Master.
Are you looking to heavily overclock your new computer? Honestly, I don't think its really worth it for water cooling unless you really planning on pushing your new computer to its limits. This by far is one of the best air coolers out there and will give you excellent cooling performance: http://www.newegg.com/Product/Product.aspx?Item=N82E168...
Well $1,000 is a nice budget to have. Overall I think you would have a nice setup. I personally would skip the water cooling and go for the Hyper 212 and take that saved money to use towards nice SSD instead. You mentioned in your OP that you are considering overclocking, if you are, the 212 will absolutely allow some nice overclocking--just not to the extreme of water cooling. I think your RAM is a bit overkill. Anything at 1600 to say 2133 would be just as good, cheaper, and honestly the difference in performance outside of some benchmarks will be unnoticeable in real world use. With the CPU and RAM you are considering, the only way you would get more out of that setup or even with lesser RAM is to upgrade the graphics card.
No because these newer processors run a lot cooler. The newer technology is able to do more but at a lower voltage and wattage, which means it runs a lot cooler. The Hyper 212 will give you significantly better cooling ability over the stock cooler and allow you to overclock. If you want to go above say 4.5ghz, then okay, go ahead with water cooling, but I don't see where outside of benchmarks you will see any real world gain from pushing it far beyond that--your GPU will be the bottleneck in games, so then you are just overclocking high to sound cool I guess. I don't mean to belittle what you want to do, but you are upgrading to an already fast processor, and with the 212 will be able to overclock over 4ghz easily without raising your temps to an unsafe level. Still, if you feel like you want to push it to the limits and your main goal of this system is to overclock, then by all means, go for water cooling because you will reach levels you can never begin to get on air. If you are unfamiliar with overclocking though, it might be best to start on air and see what its limits are before diving into heavily modifying the settings.