If I use clouding swarm, and start weaving light attack -> surprise attack -> bash, which of the 3 separate attacks will get the in stealth damage bonus?
All of them. Clouding swarm keeps you invisible for the full duration, no matter what you do. You can spam skills/basic attacks/zone chat however you like and get the 10% damage increase for all of them (except for zone chat, but CAPS LOCK helps a lot here).