Dear Levim,
this is the typical situation where I would not model that part of system in a beam-analysis piping stress calculation software, because:
1) this connection can't be reduced to a beam connection (some people uses rigids)
2) if I understood you are modeling an equipmetn, so you are modeling something that is outside piping code's scope. I only do that when I have a simple geometry.
3) it could be difficult to calculate the flexibility of that 3D asymmetrical system without a FEA.
I would stop my model to the first flange and ask to the vendor the displacements and allowables forces and moments.
Regards
Corrado Vannella
www.vannella.com