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?
I write in both R and Python regularly.  I find Python modules for writing, reading and parsing information easier to use, maintain and update.  Little niceties like the way python lets you deal with lists of items over R's indexing make things much easier to read.
I highly doubt you will gain any significant speed-up by switching the language.  If you are becoming the new "maintainer" of these scripts and you find Python easier to understand and extend, then I'd say go for it.
Computer time is cheap ... programmer time is expensive.  If you have other things to do then I'd just limp along with what you've got until you have a free day to putz with them.
Hope that helps.
R or Python for file manipulation