1) Its not the PC that needs to settle, its the user. After all that installation and tweaking, it wouldnt be surprising to come across a bad/incomplete/incompatible install here or there or a driver
conflict or a tweak gone wrong or a user error. When you start using the machine all these show up, then you iron them out one by one till everything's working harmoniously.
2) Having at least 2 partitions, one for the OS and programs and one for data makes sense. It lets you preserve your data if you need to reinstall the OS and keep the OS and programs on the fastest part of the hard drive. I'm talking about platter drives here. In any case you'll be wasting that one TB if only the OS and programs reside on it, most of us would be using just a 50gb-100gb partition for that.
3) Well SSDs are expensive, thats the only problem. Otherwise they are awesome, they're fast and boot quick. You want to improve your WEI score, get an SSD. Thats the single most worthwhile investment you can make apart from additional RAM, in terms of performance.
4) Ya, you can partition the hdd after installing the OS and programs, only thing is windows wont let you shrink the existing partition below a limit, so you'll still end up with a ridiculously large system drive. Solution is to use Partition Wizard (freeware utility) to shrink to size of your choice.