I think, given the amount of customization you're looking for, you want a linux desktop, not Windows.

I can't speak for Windows 8, but I've built a few dozen Windows 7 machines of various configurations and never had the kinds of install problems you've had. Here's how I do it.

1 - Put in the disk
2 - Boot to disk and run the installer
3 - it reboots a couple times while it's installing, but I don't care because I'm off doing something else
4 - it asks me a few questions and starts up
5 - let it run through a bunch of update cycles (which does take forever, but it's semi-automated so I'm doing something else most of the time)

On occasion I've had to install a network driver after it finishes, or if it's virtualized some guest additions but that's it. It does take hours, but they're mostly unattended hours that I can ignore, and if I want to use the machine quicker, I can skip the update cycles and just get going and let it update when I shut the machine off at the end of the day.

My latest machine, which I just built, didn't require any driver futsing.

I have no idea why you were trying to install 7 (and it sounds like your goal was to get to 8) on a 30GB SSD. I wouldn't install anything but a bare bones command-line only CentOS on a disk that small. It sounds like a couple days of your time were wasted trying to put a 50+GB OS on what's essentially a medium sized thumb drive and suffered for it.

All that being said, back in the XP days I did build a system with Program Files on a different machine and for the most part it did work, but it wasn't really well supported (even if it's supposed to be) and felt kludgy.

The Registry is one of the worst ideas in the history of computing. Nearly every time I've had something go wrong with a Windows machine that wasn't outright hardware failure, it was a problem with the registry. Registry editing really is a last resort for the bold and desperate. There's some serious voodoo in there.

So we've solved two of your problems off the bat, 1) don't install the OS on disks that are too small 2) don't mess with the registry

On to small gripes

* No decent UNIX command line. Cygwin starts slowly and is poorly integrated with the system.

True. Your best bet if you want Linux is to virtualize a linux machine or install linux or use Powershell. Remember, you aren't using a nix.

I can't get decent 2-finger scroll without a 3rd party program that is occasionally broken by system updates.

Touchpad support on Windows is lightyears behind OS X. Apple has actually turned the touchpad into something useful instead of an emergency replacement for a mouse. In Windows, just use a $5-10 2 button mouse with a scroll wheel.

* I can't remap capslock without downloading a 3rd-party program to perform registry edits.

True.

* I can't shut off the screen without installing a 3rd party program to do so.

What do you mean? Are you trying to just use the laptop hooked to a monitor and don't want the monitor on? Just set the power management so you can close the lid and leave the machine on. It's something that doesn't exist in OS X so you probably haven't thought of it.

* In Win7, all allowed keyboard layout switching shortcuts were combinations of modifiers that conflicted with productivity apps like Illustrator. Also, the layout would occasionally become "stuck" and failed to respect the GUI switcher. In Win8, they added a no-conflict key combination for switching layouts but it doesn't work in fullscreen apps.

What do you mean? Why are you trying to switch the keyboard layout so much?

* Metro. It looks slick, but it doesn't have any of the options you regularly need to access. Fortunately the old menagerie of Windows utilities is still there, just moved around.

No experience at all with 8, it looks like a version I'll probably skip alltogether as 7 is still majority supported and I don't have any compelling reasons to go to 8.

* No standard install system that lets you inspect the installer's logs, scripts, or contents.

True. Installation under OS X is much slicker and better thought out in general than on Windows. What's your compelling use case to need to do this though?

* The intimate connection between my computer account and Microsoft cloud account creeps me out.

Must be an 8 thing. 7 doesn't really have anything like this (at least that I use or care about).

* The full-screen force-quit mechanism is insane (ctrl-alt-del, open Task Manager, press Windows to reveal the Launch Bar, click on the arrow to see all system tray icons, right-click the tiny Task Manager icon (a gray box), enable "Always on Top", highlight the program in the task manager, hit "End Task", wait, hit "End Task" on the dialog box that pops up, and finally decline to send a bug report to Microsoft)

Hit Ctrl-Shift-Esc, go to "processes", right click on the problem process and just hit "end process tree". I don't know why you're doing all that extra stuff after you've got the task manager up.

* I can't use the keyboard to navigate directories that contain a mixture of files and folders because in Mircrosoft-Land "Alphabetical Order" means "Sort folders first, then files."

Why not? I pretty much only navigate in Explorer via keyboard. Why does sorting folder first (which in my and many people's opinions is far superior to mixing them up with your files) prohibit this?

It's bad enough in OS X that most of the finder replacements I've tried change the sort to folders first then files. Folders are different then files and should be sorted separately. Between music, retrocomputing, movies, and photography I manage over 3 and a half million files using pretty much explorer from the keyboard without much fuss. It's lightyears ahead of Finder in this respect.

One trick, with a folder open, just start typing the name of the file or folder you want and it'll quickly navigate down to around where the file is.

* The sub-HD preloaded desktop backgrounds (yes, really).

Replace them with whatever you want. The built in Windows picture viewer is better than OS X's (it even lets you look through folders full of pictures in sequence!) and you can right-click and turn any picture into a background.

* The ability to roll-back updates. It has never worked when I needed it to, but I like the idea.

Sometimes when your registry gets b0rk3d, this is the only way to save the computer. I don't really like it at all when I try to use it manually, but it's got my bacon out the fire on more than one occasion.