Interesting that the piston didn't come out of the bore. I think nothing is holding it in but rust, which can be severe between aluminum and iron. I would use heat to melt the rubber. I just had the same problem removing a toilet seat. I couldn't unscrew the plastic nut on the bottom. After fussing upside down with visegrips and prybars, my wife said, "melt it" so I remembered my tiny butane torch from Harbor Freight which made quick work of it.
Most manual MC's I have seen come with the brake rod, dust bellows, and plate. If you can still get a refund, I wouldn't use that cast-iron MC. Those tops notoriously slosh out brake fluid and let moisture in to cause internal rust. I prefer a modern aluminum MC w/ well-sealed reservoir. Lighter and doesn't rust to ugly. You need a 2-4 bolt adapter plate ($30 ebay). Many here use a 1980's Dodge truck aluminum MC. I used a 1998 Breeze ABS one. Booster Dewey sells as a kit for ~$95 (many posts).
