Here's your mod chiming in(for what i'm worth)...
Those settings by Stephens were good settings back in 8.0.4. But with Samba updates if you are using FreeNAS 8.2 the defaults have changed. Those settings are defaults except for the buffer size which I think is defaulted to 256k now. So if you used those settings you might be limiting yourself more than the defaults.
I know increasing the TCP window size can matter(but at the expense of CPU resources) but I'm not sure how you change it exactly. The TCP window size should be a system wide parameter(if I remember correctly), so it won't go into Samba. For most people changing the TCP window size is like trying to "overclock" your network settings. This isn't a real overclock because you still can't exceed 1Gb/sec, but it can help alleviate some bottlenecks. There is diminishing returns, so setting it absurdly high will use alot of CPU resources but provide exponentially decreasing benefits.
The only "tweaks" I have done was autotune was turned on(then reboot). It will add 3 sysctls that can help network performance in certain circumstances and with certain cards. I always recommend autotune be turned on if you have >12GB of RAM, which you do.
Based on your iperf results I'd bet you are using a Realtek NIC. Intel can give you some significant performance increase and are cheap. If you want to spend enough time with tweaking(don't blindly start adding stuff... read up and understand what they do and how they can help and/or hurt you) you should be able to get at least 750Mbit/sec from your NIC. I can't provide any guidance with this because I found it easier to just buy a $25 Intel NIC and be done with the problem. If you search the forum when people say they have network performance issues the default answer is "buy an Intel" NIC. It's the easiest answer to the problem unless you have a crappy CPU or insufficient RAM. You aren't in that category since you have a more powerful system than I do and I can saturate both of my Intel Gb ports simultaneously!