Hi all,
Thanks for all your help! I was so pleasantly surprised.
I found the 100mbps bottleneck to be the Apple usb ethernet adapter I'm using. It's not gigabit, just 100mbps. Facepalm.
Still, though, that does not solve the problem of not being able to directly connect. I'll probably go through the router through the time being, but I'd really like to figure out this direct connection interface for when I eventually go to 10gbps Ethernet. I'll try out all your suggestion in ~5 hours when I get home.
I also checked my speeds last night to make sure the drives themselves were fast enough, and was shocked to find them to be quite slow (on a relative scale). Roughly 200 mBps read/write speeds, when I know they should easily be able to get 600 mBps. I'm running 6x4TB drives on RaidZ2. Everywhere I've looked online says 600mBps is easily achieved. I know I won't be able to get to this speed on a gigabit Ethernet line, but for when I eventually upgrade to 10gb, this will be a big bottleneck. Any ideas on how to debug this? I found these speeds by using the dd commands found everywhere on FreeNAS. I'll probably go home tonight and wipe everything to Raid0 and post what speeds I see then. Might be a Raidz2 problem. Not sure.
Anyway, so those are my main two priorities. 1) Direct connection via Ethernet to the FreeNAS. 2) slow drive read/write speeds. I'll try everything you guys already mentioned for number 1. Thanks for all your help! Follow up post to come soon.