Gilbert,
In answer to your original question:
"...our ops manual states that the FMS must not be used for primary navigation below MSA."
Let me follow the logic - descent in IMC below MSA is conducted via an instrument approach and therefore requires navaids designed, approved and flown for that purpose. I am guessing that either the FMS equipment, the installation or you are not approved to conduct FMS-based approaches. So the regulator and your employer don't want you to do it, so they ban it in the Ops Manual.
But you don't accept that, so you are looking for some form of justification for violating the ban - correct?
"Does this mean that the AFCS cannot be coupled with the FMS or just that independent nav equipment must be used to determine position/track?"
As a purist, the answer is that the FMS should not be coupled to the autopilot below MSA and you should be navigating by either coupling to a suitable navaid or steering by reference to that aid. The FMS data should be monitored by the PNF/PM as part of the available data to back up the primary tracking conducted by the PF in accordance with the terrestrial navaid information.
In practice, children of the magenta pretend to monitor the terrestrial navaids while letting the FMS drive them to their destination, intended or otherwise. And they have been known to miss detecting failures of the navaid or the airborne receivers while "monitoring", as well as failing to detect waypoint and track selection errors, let alone FMS accuracy issues.
"If we define the pilot as the primary navigator rather than the autopilot, is it legal to program a pseudo-vortac to follow an NDB approach and monitor the aircraft remains within the approach tolerances?"
Whatever you choose to define as the primary navigator becomes a little irrelevant - in the end it will be the Judge who decides what actually took place and the extent of your culpability, including a few words about the difference between "reckless" and mere "negligence"!
There are invariably good reasons why the Ops Manual has bans on certain practices and why most jurisdictions have a rule requiring you to comply with your Ops Manual or face a criminal sanction.
Stay Alive,