After over a year of wishing and several hours of searching (spread out over that year) I have finally found an app for my Android powered smartphone which will allow me to add annotations and highlights to Adobe Acrobat .PDF files. The program is called Repligo Reader from Cerience and is available on the Android Market either on your phone or on the web.
P.S. I have nothing to do with Cerience. I just found a good product that meets my demands for allowing me to maintain control over my documents and annotations, and I wanted to tell people about it.