Hi guys, anyone know where the "New Project" is stored and how to edit what the layout and preferences are? It's not in "New From Template" unless I'm being blind...

The new template is called "Basic" You do not need to edit this though since you can assign any template as default in that open dialog. The old one was "Normal" and should still be there (and how you last tailored it).

You can start a new template from the current default template by creating a new project CTRL+N or open any existing template from the main menu File > Open by setting the "File of type" to "Cakewalk Template" and "Go to Folder" to "Template files (CWT, TPL)."

To save the template, from the main menu File > Save and set "Save as type" to Template and "Go to Folder" to "Template files (CWT, TPL)."

I would recommend saving the template to a new name rather than overwriting a factory template. Once saved, to set the template as the default either use the Start Screen and click the star in the upper left of the template in the "New From Template" area

Or from the main menu File > New select a template and click the "Set as Default Template" button.

I would also suggest you look into creating and using Track Templates, because those are crazy helpful for saving time AND for providing consistency in your projects.  It's just a kewl feeling when with just a small number of mouse clips, you can load up a bunch of synths in the synth rack, have their audio and midi tracks already loaded and routed, midi channels set, and even buses and aux-buses can get pulled in.
 
I use those all the time, along with a modified Normal template.
 
Best of it all to you, 
 
Bob Bone