@xyzygy: I had already had a look at the first post of that thread to get Steam Big Picture loading as a shell. However I didn't have much of a look through the comments to tell you the truth, but at your advice, I did. There wasn't a solution to my specific problem but it did give me some ideas on what I could do.
So after about 12 hours of research and a lot of fumbling about, I wrote a batch script and used it in place of the steam executable for the shell.
Just copy and paste this script into a new .bat file and call it whatever you want.
CHOICE /T 10 /D Y /M "Launch Steam in Big Picture mode?"
IF ERRORLEVEL 2 GOTO End
IF ERRORLEVEL 1 GOTO LoadSBP
CD "C:\Program Files (x86)\Steam\"
What the script does is ask if you want to load straight to SBP or not, after 10 seconds it loads SBP automatically. Press N to load windows normally. This isn't quite what I wanted but it does the job.