I custom built a desktop machine. The motherboard is populated with 16 GB. Room to grow to 32 GB. CPU is an i7-2600k. Disk is a 2 TB SATAII. Also has solid state disk on another SATA channel. It is dual boot. Windows 8 Pro and Fedora 18 x86_64. When booted on Windows 8 Pro, I also have VMware Player installed to run Linux machines inside Windows 8. That works like a champ. Windows 8 is a bit funky, but fully usable. I have Windows 7 Enterprise with 8 GB RAM, 500 GB disk, i7-2600 CPU as my "company" laptop. That is a fine machine too. The "laptop" hosts VMware Player too, so my Linux machines are all VMs inside Windows.
You want some rotating disk for large scale storage. You also want SSD so the operating system runs damn fast. Make sure the SSD is fully error checked before you use it. Fast multi-core machines are often wasted waiting on show disk resources. A good SSD solves that problem.
80% of what you wrote went right over my head. I’m just glad I have a better machine now, 50gb lasted my 5 years, so 500 should last forever, or until the asteroid strikes.