Just a quick note:
Your serial protocol should be 8-N-2 (not 8-N-1), 8n1 works like that a little because of a default setting but it will throw in an occasional bug, So switch your Mach serial protocol to 8n2, and change your Com Port2 in the PLC to 8N2 also.
Further, Unless you are using a USB to Serial adaptor you can set your Refreash rates down to 25ms from 50 they are now. If using an USB adapter then depending on model you might want to set your "Time Out" upto about 40-50ms to account for the translation time overhead.
Also: On your Brains, the Discrete "Bit-of-Word" filtering really doesnt work right (is on Brians to-do list) in Brains, I noticed you had some Inputs that where using Digit. Only if your are only looking at the very lowest bit with discrete will it work. If your trying to look at other individual bits in that incomming or outgoing word, then it doesnt work.
Also2: Another thing (little bug thing), is that on your inputs that go to LEDs, if you want the LED to "Light Up" when the input Goes to 1, then you will need to put an "Invert" lobe after your input.
One Final thing you might want to consider: When the Sepia Modbus Module "dies", it dies SILENTLY!!! so if your Modbus Coms do drop out, you will never know it other than your PLC will no longer communicate/function with Mach.
It is good to put a "Com Watchdog" function in both your Brain and your PLC ladder. If the coms do Drop (and they are notorious for doing it with USB to Serial adapters (depending on Brand), not to bad with straight serial) You can put that if a timeout from a com loop between your PLC and Brians goes for ********* amount of time then it will Estop Mach and your PLC will Kill its outputs........... (been there, done that.........)
Scott