Why do you want to model angular misalignment?If the intention is to check flange alignment,save your current file with a different name & free the concerned flange node of any restraint say connection to equipment flange or of any applied displacement & check only for WNC+H case (if you have springs & make them rigid in load case editor) OR only WNC (if there are no springs) & check displacements at your flange node.
Why do you want to use Cut short or Cut long? This is done when your spool at site is shorter or longer than the designed length (then the Powerful Construction guys pull these to join
them) or used to reduce loads at particularly turbine/compressor nozzles by Stress engineers (though its not very common as keeping track of the cut short length after every shut-down is too much of asking).
Hope this helps.