Fused charger leads

20A in the negative (black) lead should be fine. Although your charging current might only be 3A, you're safeguarding against a serious short - like touching the crocodile clip to the frame.

Most modern chargers have a safety overload cut-out anyway so fuse is probably superfluous. But, if you're wiring a permanent 12v connector into the bike, like the one that's standard on a Mk3, and using it to charge the battery, then protect the wire from that with a fuse.

I'm assuming you will not try to spin the starter motor with the charger connected.