Network Bottlenecks

I currently am coming into troubleshooting performance issues when accessing the server in a small business. There is a 48 port 10/100 switch that is 95% full and outside of thise are a small handful of 5 port gigabit switches going to various workstations. I have a RN104 (6.2.2, 4 x 2TB drives) that we use strictly as a file server with 15 or so users. Typically there are not more than 3-5 accessing this unit at a given time which is all done through mapped network drives directly to the shares in Windows (mixture of 7 and 8.1 machines).

Over the past month performance has gotten noticeable worse with no apparent cause or changes in our network. When opening a folder on a share there is a good 45-60 second delay for the file structure to load from multiple different machines. This does seem to be worse and more reproducible in 2 specific share folders that are very large.

Any suggestions on where to start looking or apps to try and help me with this?

I am considering an upgrade to a RN512 unit down the road and a Gigabit switch but that isn't in our budget right now and I have been tasked with getting performance back to the 10mbs mark we were hitting before.