Significant Figures in almost-scientific notation
Most of the answers to your questions can be found in this wikipedia article. You are right if you say: 


  I've also learned that for a number to be in scientific notation, it
  must have a stem between 1 and 10.


This is the convention in scientific notation. The number format of $0.40 \times 10^3$ is called exponential notation (at least it was called that way in a book about the programming language Fortran I'm reading at the moment): Here the number has a stem between 0 and 1 followed by a power of 10. This is quite common in computer science.
As to the significant digits: This wikipedia article (especially the paragraph "Scientific notation") contains the information you need. According to its information I would say that the number $0.40 \times 10^3$ has $2$ significant digits.