For the swept volume of each cylinder you have to multiply the area of the circular end of the cylinder by your stroke. So if you have a 5cm diameter, then the area is the radius squared time pi - so 2.5 x 2.5 x pi - then multiply this by the stroke and you get 2.5 x 2.5 x pi x 5 = 98. I've used Excel's "goal seek" feature to find the alternatives that give you the 125cc answer.

Glands where a piston rod passes through the end of a cylider are not common in IC engine designs - but they are well used in steam engines. If you can look up pictures for designs for these you'll see they often have an o-ring seal or some twists of graphited yarn as the packing.

Thor detail of piston road and gland | Flickr - Photo Sharing!

http://www.co2.pwp.blueyonder.co.uk/...ics/glands.jpg

Pump Packing Installation

You'll see in the picures there's a clamp to tighten up the packing. Some designs have a threaded ring to do the job. Your pressures are quite low so you may get away with the shaft just passing through a cloesly fitting tube.

Although you're really inviting suggestions for making your design, and not on the design itself, I'd have to say that the cam arrangement is not going to be at all easy. Perhaps you could look at this side rod steam engine, and imagine an extra cylinder on the right.

'SIDE ROD' TABLE ENGINE - Brunell Steam Model Engineering

The two cylinders would be connected by a common piston rod, and the side-rods take the back-and-forth motion off to a crank and flywheels. This would be a lot easier to make.