Difference between S3 and S4 - well I would think it is just a convention to call things S3, S4 etc rather than banana and cabbage. A Yoshi S3 may be more extream than a Megacycle S4, it just means that Yoshi had 'developed' 3 stages of tune and MC 4. I would also guess that from different 'good' tuners, there would be some equivelence. It is likely that a Yoshi S3 will give less peak power than a MS4.
Measuring lift and duration. I would look to measure the lift fitted not on the cam itself. A dial guage would be good for this, but you could do it with the depth guage feature of the calipers. It is the valve time area that changes, there is a point in lift, where lifting more does not effect the VTA, as it is the area of the port - or other feature - that restricts the flow more than the total lift. If you have a 1980's programmable calculator JR has a prog in his 4 stroke book to work this out. The duration is important and this is not just the broadness of the nose of the cam. JR goes into great detail on the measuring of valve time. He suggests that max lift needed is 0.27 X dia of valve.
Of course this could all be bollox as I have had a couple to drink...
Keep the rubber down and the leather up
R