First, when advanced spell checking is needed, the LaTeX could be converted to plain-text using: detex filename > filename.txt (note the omission of .tex extension).
Most LaTeX distributions come with detex program which simply strips LaTeX commands.

Second, when working with vector figures it might be a good idea to convert all texts to paths. Remember that eps-format does not support transparency.

Third, in order to count words in the final pdf-file use pdftotext filename.pdf - | tr -d '.' | wc -w. This will return the number of words in our file.

Finally, to generate a pdf-file that is acceptable by manuscriptcentral add \pdfminorversion 4 to your LaTeX-source.
Otherwise, if you use pdflatex to produce your pdf-file, manuscriptcentral will give a notice “failed to convert to the appropriate pdf”. Read this blog-post for details.