Here is what I found for the specs on your firewall.
Fortigate 80F and a FortiSwitch 224e POE. Block-Intra-Vlan Traffic is not enabled so all the routing will take place in the switch.
No, that is definitely not the case. Unless your switch has multiple layer 3 (VLAN) interfaces (which isn't what it sounds like to me from the way you describe it), the traffic is being routed at layer 3 by the firewall. Unless you have done some other configuration to bypass inspection, the firewall is still inspecting the traffic that transits it.
The switch is capped at 56 Gbps so I don't feel the switch is being over worked.
No, I am sure the switch isn't being overworked. The firewall doing the layer 3 routing is almost certainly a bottleneck. Bear in mind that the total throughput numbers include any other traffic going through the firewall like you general internet traffic.
Would you mind sharing your topology/config so I can get another perspective on how to setup the networking for this TrueNAS?
You can see more details if you expand the descriptions in my signature, but the key components are a Cisco Nexus 3048 with 48 10G ports and 4 40G ports. Both my FreeNAS units have a 40G connection to the VLAN that I have dedicated to the storage network as do the ESXi hosts. The ESXi hosts also have a 10G connection to the Vmotion VLAN. The client facing side connects to a Cisco 3750E stack. The key thing that keeps the storage traffic at the highest possible speed is that the FreeNAS and ESXi hosts are on the same IP network, so no layer 3 routing for that. You can get really high speed L3 routing, but that costs way more than a L2 switch. Yes, the Nexus could do the L3 routing (probably at wire speed) but I was trying to keep that as simple as possible. This would also work for me if I ever ended up with a 40G/10G switch that wasn't L3 capable.
I guess the key point is that every component through which the traffic passes has some kind of delay associated with it. My recommendation would be to have dedicated NIC's for storage in the ESXi hosts and put them on the same IP network as the FreeNAS, and connect that interface only to the switch. It could be a VLAN that goes nowhere else.