How many researchers are working in R&D departments in the US, what is
their average salary and how much do they cost to their companies. I
need: 1) total numbers; 2) industry-specific numbers (e.g. chemical
corporations, pharmacutical, biotech, etc.) and 3) dynamics of those
numbers (both history and projections). 

I did a quick search.  The following are some results.  Hope that they
help.

For the number of R&D scientists and engineers as of January 2001, see
table E-6 of http://www.nsf.gov/sbe/srs/srs02403/start.htm.  The
institution (National Science Foundation) that published this 2001
report appears to have reports for previous years.  You can contact
them for previous reports to get your historical data.

For dollars per employee, check out
http://www.nsf.gov/sbe/srs/nsf00301/tables.htm
This table is only for 1996-1997.  

Here's another report in 1998 that has some relevant info. 
http://www.nsf.gov/sbe/srs/nsf99335/start.htm.

I suggest that you contact NSF.  It appears that that do surveys each
year about R&D expenditures and R&D employment in industries.  So they
may have exactly what you need.

The comment made by dolaimo led to                                    
                               the 116 page PDF document which seems
to contain all the information you require....Perhaps a researcher
will be willing to extract the information for you from this document.

      http://www.nsf.gov/sbe/srs/nsf02312/pdf/secta.pdf