Christy,

Were you aware that one Martha Lilley filed for and received a CSA pension for your gggrandfather ? Well, she did. The file is number 29792 in the CSA Pension Applications in the Texas State Archives. Ms Martha was residing in San Jacinto County, Texas when she filed the application. You can request a copy of the application from the state and the applications usually have a brief summary of the members ( Ben F Lilley) service. So try that . I also see him listed as Capt. Lilley , head of a Company of Pardoned Deserters. Since this is such a small group, you're probably really going to have to dig to get the real good info. But let me just say this about your concerns about his status as a deserter; if I know anything about us Texans , it's that we don't honor traitors and deserters with a pension !! I know you'd like to see a piece of paper or a document that says that B.F. Lilley was an honorable Son of The South and a true Texas patriot but you may not find that . You really need to see his compiled service record to get more of the facts , but I'd be real surprised if the Great State of Texas would grant a pension to a widow of a man who was considered a Confederate deserter. These just wasn't enough cash laying to do that, plus , there were still too many politically powerful CSA veterans in high office( Gov Sul Ross, Gov Sayers, etc.) to think that they'd let it slide through.
Sorry for the treatise ; but I hate to see you spend a lot of time and effort in trying to "clear" your ancestor's record. All the best, CRaig