The 2012 annual report on the LEGO Groups site states the following:
Research and development activities
Each year, new launchings account for approximately 60% of the LEGO Group’s sales to consumers. Therefore, the Group has considerable development activities, comprising anything from trend spotting and anthropological studies to the actual development of specific products and campaigns. Approximately 160 designers from about 20 different countries make up the creative core of product development that is mainly based at company headquarters in Billund, Denmark.
It's hard to quantise exactly how much of each set goes into the various different aspects you're asking about as different sets will have different margins on them. Taking some of the numbers in the report however, you can see things like:
On Revenue of 23,000mDKK:
- 6,800m was spent on "production costs" (about 30%) - these are defined as "raw materials, consumables, direct labour costs and indirect production costs such as maintenance and depreciation, etc.". These are further broken down to include:
- 4,400m on Raw materials and consumables
- 1,500m on Licence and Royalty expenses
- 1,200m was spent on "other operating costs" (about 5%) - these are defined as "[including] royalty and research and development costs". This is further broken down to include:
- 451m on Research and Development
- 6,100m was spent on "Sales and distribution expenses" (about 27%) - these are defined as "costs in the form of salaries to sales and distribution staff, advertising and marketing expenses as well as depreciation, etc."
In terms of where parts are made, this answer covers most of it, but as you rightly note, Minifigs, and some painted parts now come from China. In terms of R&D, this answer talks about how new pieces could come about.
Updated: Some of the actual break-downs in here come from the "2012" columns in the 2013 report.