Diagnosing windows file server performance issues, utilities?

We've been having a ton of performance issues on our windows server 2008 R2 file server in the office of late. We've been trying to pinpoint the issue for ages but can't work it out.

We have 4 virtual machines running server 2008 r2 on top of a VMWare server. We have two physical hosts, and use a Netgear ReadyNAS (we're a smallish business) to hold the VM's. This was all working fine until late last year when we started noticing our shadowprotect backups were running at 3-4MB/s instead of 40-60+MB/s.

We've tried a ton of different things, and have had trouble pinpointing the issue as sometimes the server will run great (often just after we reboot it) but then randomly it will start going slow again. We've tried moving it to different hosts/NAS's (we have a dell nas we tried as well), but nothing seems to help permanently.

Right now, my file copies are going at 6MB/s, on a gigabit connection to the server. Another VM on the same NAS is running at 40-50MB/s copies. We recently rebuilt the VM to try and fix it but no go.

I've got the feeling that something/s on the network are hitting the server pretty hard, perhaps using the file server too heavily (we use Revit and AutoCAD, which could be network intensive), or something else rogue starts thrashing it.

My question is, how can I diagnose this? When I run the performance monitor to see commonly used files our CPU goes through the roof (it already sits on 50% just from 'system' usage) so we can't run it for an extended period of time. I've tried process monitor but it's hard to sift through.

I'm just keen on knowing what network traffic is causing the most disk/network load, how can I monitor this? Do you have any other suggestions for us (apart from buying a SAN, I asked for one and was rejected...)

Our file server is a backup DC as well, could this affect anything?