2.5mm isn't much. It would be 1.75mm each side. What stroke is it? If it's long stroke chose pistons carefully. Ed V's B44 pistons are great because the skirt is high. Other B44 pistons can have a lower skirt and come out of the bores at the bottom. His are short and I don't know any that are better quality.
Otherwise cut or shape the bottom of the piston. I did that putting T120 pistons in a T150.
The piston will slide across on the pin. Has it room to do that? 1.75mm isn't much. I've seen A65's with the crank so badly aligned under the bores the rods so hard against the piston bosses it spun the L/end bushes out.
I cut the tops off old pistons to check that on mine, the alloy rods are wide. I doubt it matters much as long as it has some clearance.
I would not ever cut that crank. You can with a stock one because the halves spigot into the new flywheel and keep it true. Early and late cranks do vary in width? Which doesn't mean that matches any really, but worth checking. Pins would be spaced the same though.
This shows this type of B44 piston. On a std stroke crank there is lots of room. This one isn't good on the other side when cheap Nicasil came off. It can be cheaper just getting the best job even if it costs a little more. If you use those pistons you have draw on them with a felt pen and cut them off. It doesn't look like it's hitting by much.