I briefly looked into putting together a pneumatic press. I stopped when our lab director said in his experience pneumatic cylinders (at least the lower price ones I was interested in) leak quite a bit (I don't know what experience he has, but I'm sure he's got more than me). Because in pressing cheeses you need sustained pressure (6 hours is pretty common, 12, and even 24 are not uncommon), a leak in the cylinder, depending on the size, could lead to the compressor running frequently--not necessarily a problem, but possibly depending on your situation.
1. As for cylinder size, it depends on what you're looking to make. I've seen pressure called for from 2 psi upto 40 psi, but it seems that around 6 psi works for most of the cheeses people make. I think I'd figure out what size cheeses I was going to make, determine the maximum pressure for the cheeses I'm interested in and size accordingly. If I were just winging it, I'd shoot for 10 psi on the biggest mold I plan on making.
2. A 12 inch stroke is pretty big for single cheese. If you figure that from a hand pressed pile of curds to a solid cheese you lose about 1/2 the height (I'm not sure that's exactly right, but I think it's close to what I observe), a 12 inch stroke could be used to make a 12 inch tall cheese in a 24 inch tall mold. If you plan on stacking and pressing multiple cheeses at once, a 12 inch stroke could let you, depending on your mold configuration, press a 4 or 5 cheeses that are each 1 1/2 - 2 inches thick. Either way, that's a lot of cheese.
Hopefully, someone with experience with a pneumatic press will give you some insight...