I would recommend aligning the sides as you fit Bulkheads .The plastic is NOT the same thickness throughout the model . It's a fact of life here .You can adjust the bulkheads easier that trying to align the two halves with any kind of heat .
If you have a LARGE machinist Micrometer then you can measure the thickness throughout and sand to your heart's content . This is usually is not the case .
If you carefully build your bulkheads and interior to fit as an open sided tube That will slide into the hull without binding Then you are halfway there . Then you can fit Shims of .010 into the hull between the interior and the hull till everything lines up .
This is the way I do all client "cut away' models . It's easier and looks fantastic when done . Plus , leaves room for adjustment as you add more parts . T.B.