If you must use matlab, I would create "fake points" to make the grid a regular shape, and give them false rain values (such as NaN). I would then edit the plot in a postprocessor (photoshop) so that Only the irregular shape appears.
The spacing of the grid does not matter as its specified via your vectors.
However, that will treat lon and lat as x and y coordinates on a rectilinear grid. To plot with a projection (N.B., WGS84 is not a projection. You'll need to figure out exactly what you're after with more clarity), you ideally want the Mapping Toolbox. I'm not an expert on that, but it should make projected plots relatively straightfoward.
If you don't have access to the Mapping Toolbox, then you could spend a lot of time faffing with coordinate transforms to do what you want... but my advice would be to spend the time learning the basics of a GIS package instead (QGIS is free) and use that to do the job.