The third picture of step 8 shows a PCIe connector, which would take a custom cable to attach to the SSD. I fully expect iFixit to eventually sell an installation kit with this cable, along with mounting hardware and tools.

To answer your original question, the 256GB flash is attached to a PCIe port, and is mounted to one side of the tray in step 13. You should be able to add either an HD or SSD to the other side of the tray, and attach it to the SATA port. You'll likely need to get a special ribbon SATA cable, which I'm sure iFixit will eventually sell, along with any mounting hardware and tools you'd need (like the torx6 security driver).

Depends on what you care about. The new ones should have slightly better single-thread performance, better graphics performance. Also, the new systems have faster I/O (2x Thunderbolt2) and can drive a 4k display out the HDMI port.

The way I use it, I'd rarely miss quad-core.

Flash does not "look like" RAM, even though it is built from silicon. To the system, it looks like a very fast HD, but not as fast as RAM.

Flash is connected either to a SATA (like an HD) or PCIe port. RAM is connected through the DDR contollers.

Yes and no. Some apps simply need a lot of RAM, and if you run a bunch of these concurrently, you'll definitely feel the need for more of it. SSD, or even PCIe flash, is "further away" than RAM, and takes longer to read/write. Think of it this way: RAM is directly connected to the CPU, but HD/SSD/flash is connected thru the I/O subsystem.

Somewhere, I think it was Instructibles, showed how you can use a regular slotted screwdriver on a torx security screw. I've tried it, and it works. I would imagine a small jeweler's screwdriver will fit in a torx 6 security screw head.