As a machinist with access to a dynamic balancing machine, i'd say yes, balance it all! You'd be surprised how many expensive flywheels and clutch covers are a mile out. We've just balanced a HKS 200sx stroker crank and it was so bad you could feel the vibrations in the workshop floor!

Get the crank done, then balance the pulley, then the flywheel, then finally the cover plate. Balance the rods end-to-end and balance the pistons too.