I had a similar issue with MOD13Q1 data. The following steps will allow you to get data in one area. You can then use the same steps with multiple files to create a time series. The full script that I used to plot satellite data timeseries and produce a map is linked here.
Extract horizontal and vertical tile coordinates (h, v) from the file name.
Loop through each line of the data structure to store the variables in a table.
Reproject the sinusoidal coordinates to latitude & longitude with h and v.
Load a kml file of your desired area. This can be made in Google Earth.
Crop the data using "inpolygon".