Greg,
1. A desktop system is a good choice for performance
2. Don't have a view on particular brands. Have been burnt by most of them at some time
3. Skylake is the current latest. Early next year Kaby Lake desktop CPUs will be available but will only be an incremental improvement
4. Lots of memory is good. I have 24GB in my 6 year old desktop system and it is perfectly adequate for very big integrations in PI. Sounds like CCDStack isn't as efficient. Quad channel DDR4 will give max performance with 4 slots filled (one channel each.) 8 slots is good if you decide you need more RAM later.
5. Lots of HDD makes sense
6. SSD for your boot/Windows disk will certainly improve boot time and application start times.
7. Some power & cooling headroom is useful
8. You don't need a fancy gaming card. Have a look at the Nvidia Quadro range of desktop workstation cards (you don't need a high end one.)
9. No idea what this is. SSD makes a big difference to program start times. For processing you won't care that much since you'll be running the same program for hours, or days
Cheers,
Rick.