Optimise the system for large files

Does anybody have any tips for optimising the system to handle large files? For us a small file is 30MB a large one is >40GB.
We mostly use ftp to move the files and we see that the system accepts data for a while at anything up to 60MB/s ( Task manager network speed on the controlling PC) but then the data transfer stops for many seconds, sometimes 30 or 40, and then it continues.
If the ftp speed is limited then the data rate is constant and smooth.
We only handle these larger files.
Thanks