Christy,

Looks like I found a little extra time. If you have not done this , go the online version of the Handbook of Texas www.tsha.utexas.edu/handbook/online/articles/index/new.html
then , select for a subject William Herbert Beazley. There is a good bit written on him and there is a reference to his work with the "deserters" . I don't think the text will turn up anything that you don't already know; however, the references in the bibliography may provide some new areas for you to explore.
By the way, I checked for Lilley's Company of Pardoned Deserters in Stewart Sifakis' "Compendium of Confederate Armies ...... Texas " as well as " Texas in the War" by Brig Gen Marcus Wright, CSA ,annotated, compiled and edited by the late Col Harold B. Simpson USAF . I did not find any reference to your ancestor's unique company of Pardoned Deserters. W.H. Beazley may be your best "trail" to follow for anything he may have written about Capt Lilley and his boys. Good Hunting, Craig