So, onto the questions:
1. Is there a recent, detailed guide for step-by-step instructions on assembly and first boot? I've found a few here and there but I'm nervous about this process.
2. I have heard that even the Z77 series MBs don't natively clock RAM to 1600 MHz. How do I change this setting to make sure my RAM is being fully utilized?
3. Is there anything in my build that is glaringly wrong or stupid? I've ordered the pieces already but could return/exchange anything.
4. What is, in your opinion(s), the optimum fan configuration? Right now I'm thinking 2x120mm on the front blowing in, the 140mm on the side blowing in (mostly to spot-cool the GPU), and 1x 120mm and 1x200mm on the rear/top to exhaust, plus the PSU exhaust. I know it's probably airflow overkill, but I've had overheating issues in the past and don't want to repeat them.
5. What is the best order in which to install everything? Each guide seems to have a different answer; some say to install the CPU and RAM onto the MB before installing the MB, for example, while others say you should put the PSU and fans in before anything else, etc. So I'm just a bit confused.
6. Any tips and tricks for installation and boot? I'm going to have to spend a lot of time on the PC trying to get my SSD boot/program drive plus my HDD storage drive configured right.
Your computer components look fine to me. Have you tried looking on YouTube to find a video showing how to assemble a computer?
I'm sure there are more than enough qualified forum users who can give advice on assembling your computer but here are the steps I took.
For every component, physically look at it to see if there is any damage such as broken corners, bent pins, color irregularities and such.
Start with the case and remove any cardboard boxes inside of it, there usually contain your hard drive mounts, screws, standoffs, zip ties, and other things needed to put everything together. Read the manual and install the standoff's (small metal pieces that have threads on one end and are able to accept screws on the other) depending on the form factor of your motherboard, probably ATX in your case. Also install the I/O plate from your motherboard onto the I/O slot on the back of your case.
For your CPU, it is critical that you read the manual on your motherboard and CPU since all chips have to be put in a certain way, usually by matching up arrows on the corner of the CPU seat.
It's personal choice whether you want to install the RAM sticks and CPU cooler outside of the case or inside the case, I've done it both ways. Space constraints should be considered since in my case I had to install all my fans before installing the CPU cooler since I use a Hyper 212+ and it has a big heatsink. I would personally install the PSU after the motherboard but it's personal preference.
Which ever way you decided to install the CPU cooler and RAM, you will next need to slide the motherboard on a slight angle so that the I/O inputs slide through the designated holes in the I/O plate and then rest the motherboard onto the standoffs. There are holes on the motherboard that correspond to where standoffs should be so use screws and secure the motherboard in place. Hand tight should be enough to secure the motherboard; there will be holes on the motherboard that don't get screws since not all cases are made the same and you will usually catch enough standoffs to hold it in place, mine has about 6 or 7 screws holding it in place.
I don't know if I should continue since it can get quite lengthy but I'll let other forum users weigh in.
Be sure to not stand on carpet while you are installing the components as static electricity tends to build up and any static discharge at a component will mostly mean dead component.
After successfully placing the CPU chip into the socket, you'll probably want to move onto installing the RAM sticks. Most motherboard now-a-days use a dual channel configuration in which you will need at least two RAM sticks placed into two RAM slots, check your motherboard manual to figure out how your manufacturer decided to label the RAM slots. To install RAM sticks, press the tabs on the top and bottom of the RAM slot so that they are lowered and ready to receive the RAM sticks. The RAM stick will have a space along the opposing side of the heatfins which helped to orient the RAM stick since it will match up with the RAM slot. After you figure out the orientation, press the RAM stick until you hear it click into place, usually by pressing down on the RAM sticks on the top edges.
Check with your CPU manual on how to install the stock CPU cooler and make sure to plug in the 4 pin female connector coming from the fan of the stock CPU cooler into the CPU_fan 4 pin male connection so that the motherboard can control the CPU fan. Since your using a stock CPU cooler I'd imagine there is already pre-applied thermal compound.
To install your graphics card, being by removing the appropriate PCI slot covers from the back of the case, usually two or one. Now take the graphics card, which will be inserted into a PCI x16 slot with the plastic shroud upside down and slide it into the PCI x16 slot. There may be a small tab on the PCI x16 slot that "secures" the graphics card so you may or may not hear a small click noise.
The CD/DVD reader and hard drives can now be installed if you want, just make sure to read the case manual to know how to do it properly. For your SSD, you'll probably need an included adapter to fit it in if your case doesn't make room for it.
The PSU mounts on the bottom back of your case so secure it in place with screws and that should be it for the PSU. Now here comes the fun part. Your 560 Ti needs two PCI-E power connections coming from the PSU so they should be label as "PCI-E" or something like that. There is a main 24-ATX power cable coming from the PSU that needs to plug into the 24 pin header on the motherboard, usually above where the SATA headers are on the right side of the motherboard. There's also a CPU power cable coming from the PSU that needs to plug into a connection somewhere around the CPU socket, I believe it's a 2x4 or 2x3 connection. Check with your motherboard manual while you plug things in to make sure everything is oriented correctly. Aside from some SATA connections and molex connections, those three connections should be the major ones. I'll explain those if you want since I don't know how much you know already.
There are 3-pin headers on the motherboard that you can plug the case fans into if you don't have a fan controller so check with the motherboard manual to know exactly where they are. There will also be cables that come from your case which should correspond to any front side USB ports, sound ports, power switch, reset switch, and anything extra that your case comes with. Follow the motherboard manual to figure out where they need to be plugged in and you should be fine.
If there's anything else that you want to know about then drop a reply and I'll see what I can do.