How much progress have you gone with this. Navigation would be a huge challenge for end users which is how I found this thread. Also the longest thread I have stubled upon which means something is missing in ERPNext.
I needed some context menu for a doctype which is where the search started. for instance, if i was in Selling, I should be able to see all the reports and custom reports in the side bar and not all the module lists which is of no importance to me. Surprisingly, the training video has that feature but the install does not. I did a post of this here Access to custom reports
So, how much work have you done on the UX? I would really like to know and hopefully contribute my one cent.