Mouse scrolling I do with the firmware, since that’s an option using Key_mouseScrollDn and Key_mouseScrollUp. I replaced page up and page down with these options. BTT can also do this, but it’s nice to use the firmware where possible. I’ve found the scrolling to be a little inconsistent between apps, but it’s servicable. At some point I may look into other options for greater consistency.
Switching spaces is actually built in to Mac OS, those shortcuts are just ctrl+left and ctrl+right, or you can use ctrl+1–6 to switch to certain desktops. If those don’t work for you, you may need to enable them in system preferences, under “Keyboard > Shortcuts > Mission Control > Mission Control”. You can also rebind them there.
Everything else is done through the magic of BetterTouchTool!
For app switching, there are plenty of different ways to do it, and I based mine on this thread. Basically, I mapped right ctrl to hyper in the firmware (cmd+alt+ctrl+shift with one-shot), and within BTT set up shortcuts that open (or switch to) my most commonly used apps. hyper+f for Firefox, hyper+o for OmniFocus, hyper+s for Sublime Text, etc. The nice thing about using hyper is you don’t have to worry about overwriting anything, so you can use whatever shortcut makes the most sense to you.
As for window switching, you can set up “Snap areas” in BTT that are triggerable via hotkey, so I set up the 6 different window positions that I tend to use, and I use “hyper+1–6” to snap the active application to that position. These areas are also tied to certain screens, so if you have multiple monitors, this method is way faster than drag-and-dropping. This was a big upgrade for me: I’ve tried numerous window management apps in the past, and this is better than all of them. I don’t need any bells and whistles, just a way to snap everything into place quickly and effortlessly.
I’m actually currently working on a series of articles that better explain how to do this with BTT, but I’ve only published the first article so far. If either of you want more detail, I will have all the details written up there in a few weeks 
In any case, this may sound like a lot of work, but it’s definitely been worth it for me. I’m using my computer much more efficiently now, experiencing less pain in my arms, and able to focus that much more on my work. I won’t be going back to a regular keyboard anytime soon.