I left a company this year and would like to convert my 401K into a ROTH (obvious tax implications). Will this affect my FAFSA numbers?

Yes it will, for the tax year that you did the conversion, since it will increase your adjusted gross income.
If you did the conversion in 2012 it will affect your FAFSA for the 2013-14 college year.
However, you should contact your college(s) to point out that you did this conversion and ask them to consider adjusting the results. They don't have to, but they might since it is essentially a roll-over and not truly income to you.