To support an MTU of 9000 across the network you'll need hardware that supports it. When we had BT Infinity installed the BT "Business" Hub refused to support Jumbo frames and as such would not communicate properly with my server or MacPro. In the end I replaced it with an Asustek RT-N56U.
While quite expensive at £80, it supported everything I needed and far outperformed the BT hub on the WAN port. With the BT router i was getting 30mb consistently on a 40mb connection. As soon as I replaced it with the Asustek, the speeds went straight up to 39.9mb (I'm still chasing that extra 100kb/sec).
BT's explanation was that I was using the internet connection too much and stressing out the BT Business Hub. My response was a) I'm not the right person to make such incredible claims to and b) It's not exactly "Business" class for a router to be outperformed by one person and one server.
With a decent cat6 network & managed switch, you might find that you can manage without jumbo frames, as having them enabled is an all or nothing situation. If you have one link in the chain that doesn't support them then it can bring that device to a standstill.
Regards