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?
Know where the time is being spent. If your R scripts are bottlenecked on disk IO (and that is very possible in this case), then you could rewrite them in hand-optimized assembly and be no faster. As always with optimization, if you don't measure first, you're just pissing into the wind. If they're not bottlenecked on disk IO, you would likely see more benefit from improving the algorithm than changing the language.
R or Python for file manipulation