I want to do a time series analysis of NDVI using MODIS dataset by first extracting the NDVI raster values with MOD13Q1 (250 m spatial resolution and 16 days temporal resolution), 

How to handle these many images, and how to present them in results?

A single image contains 11 subdatasets. i know i have to use the first image from the modis raster for my NDVI by scaling to 0.0001. but i tried mosacking* the raster tiles as my study area is bigger than the tiles downloadable. i realized after mosaicking* the value ranged from 0-250 ( initial range was-1999/2000 to 7000+), with the image showing almost nothing or few dots of black images

How  i derive my NDVI values for my complete area and display the maps accurately. is there a best software that can do this mosaicking*. what am i supposed to do fist?, mosaic then scale to the factor of 0.0001 or scale then mosaic?. please i need help in this regard. the software i used was ARCGIS 10x