I swear to god I give up I really do, the Amiga is one complicated computer I have been building and repairing pc's for over 19 years and I am A+ Certified so I am no noob when it comes to computers but this system is driving me around the bend it really is I feel like throwing in the towel 
I've been building and repairing PC's for over 30 years and have a degree in network engineering, and the Amiga is still complicated. But putting it into perspective, try doing the same thing on a MS-DOS computer from that era. Windows installers make us forget how complicated everything used to be!
That being said, I'd suspect it's a Mediator issue or a problem with your LAN card. Perhaps some obscure Mediator update that's still missing, or a driver? 3.9 itself is pretty easy, but when you start bolting on all the extras needed for a high end system, it can cause a few more grey hairs.
Good luck!
