Ethernet components location
I would simply put an RJ45 MagJack on your circuit board right by the PHY. Then use an internal CAT5 cable to go to a panel connector. The panel connector could be one of these (although other options exist). 

 

The above pictured connector is an inline coupler that permits Ethernet to pass through into an enclosure and maintain an IP67 rating.

If internal enclosure interference is an issue you simply use a shielded CAT5 type cable with the appropriate metal covered RJ45 plug ends. The above connector can be configured as a shielded unit on the inside with a shielded pigtail CAT5 cable.