First, subract the base + fog value from the readings, since you are only interested in image density, not the background density. Zone 0 will be 0.0, Zone I is .07, Zone II is .19, etc. if you are using .37 as your B+F value.
The reason that the space between frames might be different from a clear frame is probably due to normal sampling error, although it's possible that there really is greater density between the frames due to infectious development or some sort of adjacency effect. It's not a big deal.
Also, just so things make sense in terms of other things you might read, you should include the decimal point in your density readings. They are .37, .44, etc. through... 2.06. These are standard logarithmic units of density. A difference of .3 is equivalent to one stop. You'll notice that this is the same system that is sometimes used to describe neutral density filters--.3 is one stop or 2X, .9 is three stops or 8X, etc.
The easiest way to plot the values is to make a graph with the zones from 0 to XI along the X axis and the density values on the Y axis.