I've done this before. Made a nice pistons stopper to go into the spark plug hole to get true TDC. And had a magnetic degree wheel cut onto a magnet to stick to the OEM crank pulley. It's a bit of a tedious process cuase you need fairly long dail gauges and also two people makes it easier. But in the end you're kinda shooting in the dark, as each motor likes different things.
My plan when re-assembling the motor is to get some idea of were about piston/valve interference occurs, mark those combinations off and then take it to the dyno and mess around within those parameters.