Hi there. I think I might be able to give some valid input.
First up, if you're planning on using the same machine for 5 years as a 24/7, high-availability server, you might want to point yourself to server-grade hardware, namely on the motherboard front. Supermicro is usually very well recommended. Also, you probably want a Xeon CPU, if you're going the server motherboard route.
Now, that being said, it should be noted that I had an ASRock 945GZ-based motherboard and a Pentium D 805 as a 24/7 server for almost 4 years, with power outages comprising about 75-90% of all server downtime for all those years. So you might be able to pull it off with regular consumer hardware.
As far as storage goes, if you think you'll need 9TB in 5 years, I'd re-think your strategy. As a rule of thumb, at least double what you *think* you'll need. My data storage needs went from <1TB to 3TB in just a bit over a year, and I'm stretched REALLY thin with my current 6TB of storage, only a year later. Even my planned 10TB upgrade (long overdue, I might add, and it was just last year I upgraded to 6TB) is making me feel uneasy, it will be only a stopgap solution... Data storage needs do NOT grow linearly, it seems there is a really big data hoarder inside each and everyone of us.
Also, a single big disk/array for OS and data might not be a great idea. While I do run a WHS machine with a single large OS disk, which has yet to show signs of any aging problems, one or two smaller (maybe even 2.5'') OS drives (RAID1 if two, for improved availability) might allow better I/O results and lower power use when idling (since the big data drive(s) might be able to spin down). It all depends on how much you want to spend, though, multi-HDD solutions are inherently more expensive.
Now, for the specific answers you need:
1) ATX or uATX is primarily a question of taste. It should be noted, though, that while ATX boards tend to be more expensive, they usually have more expansion capabilities, both on the add-in card and storage controller departments. You'll be hard-pressed to find a cheap uATX board with 6 SATA ports (and good luck finding one with 8 or more...), while most ATX ones with less than 6 ports are rather rare.
If you're lucky, you'll be able to get a uATX board with two PCIe 4x+ slots, plus one PCIe 1x slot, which can boost your maximum number of SATA ports to at least two dozens (6 on the PCB, 8+ on each long PCIe slot, plus two more on the PCIe 1x slot), so uATX might be enough, but plan accordingly. I didn't, and as so my current low-power NAS is limited to 4 SATA ports on the PCB, one PCIe 1x slot and a single PCIe 16x slot I don't even know whether it supports non-GPUs or not.
2) RAM is cheap nowadays, and provided your software can handle it, more RAM will allow less HDD access. 4GB is what I use for my WHSv1 machine (I don't use WAMP, btw, only storage and downloading services), no complaints there, though it limits how much data I can move around before caching sends LAN transfer speeds to the ground (around 3GB).
3) It depends on what you want to do. Since I'm using WHSv1, I use file duplication to handle availability, so single drives are fine. RAID or JBOD have their inherent benefits and downsides (though if you go RAID5 or RAID6, you definitely want a dedicated *REAL* RAID card, software RAID on Intel/AMD chipsets and cheap controllers gives lousy speed results). Read up a bit on RAID.
That being said, I'd still stick to the small OS+big data drive combo.
4) 5400rpm is fine for serving files (even over the Internet, to 4 different users simultaneously), and from my WHS experience, streaming locally to 2 PCs at the same time doesn't really pose a problem, even with high-bitrate content. Plus 5400rpm drives have lower power requirements.
7200rpm+ (or SSD, if you can fit your database inside of it) is better for database accesses (and booting an OS), because of lower latency and better I/O per second performance. Though since it's not a critical system, nor over-accessed, and you don't mind waiting a bit more for the OS to load, you might be able to get by with all-5400rpm drives.
5) Besides the XEON idea up above, an i3 might be enough, though an i5 will give you two extra real cores, twice the cache (probably good for the webserver part), Turbo Boost and the AES instructions, which might be used on your WAMP (not sure on that one, though). But, for the record, my Celeron E3200 doesn't really feel limited on my current server, so on light loads the i3 should suffice.
6) H67 or Z68 motherboards should be fine (so you don't need an extra GPU). Maybe
this (H67, should be cheaper) or
this (Z68, 7 SATA ports!)? I'm a uATX fan, so those are uATX, and based on a quick look around (I'm more of an ASRock guy).
Phew, that was one long post. Hope it helps, though.
Cheers.
Miguel