Does the refinery not specify any bolting guidance for the contractor to follow? They let them use random handbooks? Who knows the basis for those specified torque values? Targeting a stud stress with no regard to gasket style and dimensions is an outdated practice.
In terms of pressure loading...
I am not sure what code of construction you are using but an example of an elastic-plastic ratcheting procedure is discussed in ASME VIII Div. 2 Part 5.
For this you essentially use an elastic-perfectly plastic material model with isotopic hardening. This is conservative relative to kinematic...
Explicit integration is only conditionally stable; does adjusting your minimum time step help?
How are you doing your differentiation in the subroutine? Accurate differentiation can be important for convergence.
Also -...
326.3 states the design, materials, fabrication, assembly, examination, and testing requirements of this code are not applicable to components listed in table 326.1 i.e. a B16.5 flange.
Seconding what Ed mentioned.
Bolting procedures, refer to ASME PCC-1 for guidance on flange assembly.
Gasket selection, I would try CMGC (Grafoil) or GMGC (Kammprofile)
If the leak was never repaired why did it just start coming out of the patch plate weep holes? Was the crack repaired from the inside?
Do you know why it is cracking? SCC? Fatigue?
Anyways, I've had much better success with performing a through-wall nozzle replacement than using a new shell...
What is the material of the base and overlay? Operating temperature? Do you use controlled bolting practices?
Did you consider sending the flange to a lab for a failure analysis? Are you going to do weld repairs? PWHT? Hydrogen bakeout?