The data plate on the boiler probably lists input BTU and output BTU....output/input is a fair approximation of the efficiency.
Depending on the brand, some of the mod-con new boilers are over 94%. You'd want to do a heat load calculation. You probably can use a smaller one for the middle apartment since it has much less in outside walls. Depends on the layout, windows, etc. All of the mod-cons that I've looked at use pvc for both intake and exhaust. There's often a very fixed maximum length for these and you have to be careful about where they exhaust and intake are - you don't want the intake of one to be sucking the exhaust of anohter. This includes proximity to things like dryer vents, windows, and doors.