I have 4 reasonably complex r scripts that are used to manipulate csv and xml files.  These were created by another department where they work exclusively in r.  
My understanding is that while r is very fast when dealing with data, it's not really optimised for file manipulation.  Can I expect to get significant speed increases by converting these scripts to python?  Or is this something of a waste of time?
My guess is that you probably won't see much of a speed-up in time.  When comparing high-level languages, overhead in the language is typically not to blame for performance problems.  Typically, the problem is your algorithm.
I'm not very familiar with R, but you may find speed-ups by reading larger chunks of data into memory at once vs smaller chunks (less system calls).  If R doesn't have the ability to change something like this, you will probably find that python can be much faster simply because of this ability.
R or Python for file manipulation