Those 2 dowels today are often a little rusty, making them grip the cylinders real well! The small slots you've found are there for wedging, but I only tap in a (wide as possible to fit the slot width) screwdriver to break the gasket seal with them. They are about 1/2" deep, so don't drive in very far: they are just there to break the gasket free.
If the engine still turns over, you'll just have to break the gasket to get the cylinders free to pull off. You can have a machine shop clean off the gasket (mine costs $100 for this work, though), or use a fresh razor blade, a torch, and/or gasket softener to get it free: it's been glued closed for 50 years!