Nimon
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Two identities is fine if that is simpler. Alignment for this can be across the spectrim really, as a veteran I can tell you that people from all alignments fight side by side in war. Some friction might arise in the groups between the more extreme alignments, CE that approves of torturing and what not to a strict LG that might believe that against his code ect. Hopefully there can be some roleplayed resolving of the situation if that does arise.
Prestige classes from the sources listed are fine, but lets stick to those books which should be sufficient. Core,APG,Ultimate Magic/Combat and Inner Sea World Guide.