The analysis is generally done for the ends plates only, and includes pressure load, gasket contact load, and bolt loads. You can do the analysis via FEA if you can conclude that the design equations provided in Section VIII, Div 1 do not strictly apply, in which case per para. U2g, you can use some other method (e.g. FEA). When doing FEA, you would normally evaluate the stresses, using Section VIII, Div 2, Appendix 4 for guidance, but using the Div 1 allowable stress.
One point of note is that you will probably find a distribution of bolt loads that is not uniform, and suggest you consider that in design of the bolting.
