Moving the crank pin out to lengthen the stroke will increase the leverage that the reciprocating masses of the con-rod and pistons exert on the crank which in turn will alter the balance factor of the crankshaft.
Put very simplistically the balance factor is the percentage of the mass of the reciprocating parts compared to the mass of the crankshaft bob weight(s) and is typically between 50 and 60%.
The crank would need to be re-balanced to bring it back to OE spec.
Another factor to considered would be if additional mass, whether this be to pistons or rods, is added following (say) re boring to increase capacity. It will not only alter the balance factor but also the loading on the rods and crank at top and bottom dead centre.
The pistons of my 1300 only weigh a few grams more than OE, but to keep the same loading the revs need to be reduced by approximately 300 rpm.
As suggested above, it is a good idea to match the inlet stubs with the inlet ports. First job is to mark each stub so you know which port it is matched with.
Once you have removed casting marks and any other lumps and bumps and the ports line up then make sure that you leave a relatively rough finish to the port (i.e. DON'T polish them). This will encourage some turbulence which will discourage the air/ fuel mixture from 'pooling' on the walls of the port.