Perhaps it would help you if you knew more about how the Compiled Military Service Records were developed.

In late 1870s-1880s, after all of the records from the Civil War were obtained/submitted to the U. S. Department of War (namely, all of the records from the Union armies (regular and volunteer) and the Confederate records that remained from the Confederate armies--keep in mind that during the evacuation of Richmond, the Confederates burned the records that resided there--the War Department brought 50 former Confederate officers and 50 former Union officers to Washington to go through and verify the all of the records. After working with the records for about 28 years, the primary output of the officers' work was the Official Records of the War of the Rebellion.

During their work, the officers also assembled and made lists of all kinds of data--everything from hospital records, prisoner of war records, muster rolls, etc., for individual soldiers. The major output of this ancillary process was the Compiled Military Service Records for both Confederate and Union troops. In short, the officers pulled together all of the information available about an individual soldier and assembled it into his Compiled Military Service Record.

Understandably there may be gaps in the information, but those gaps occurred because the information was missing from the original records.

As far as the "D" in the upper left hand corner, that is probably a file guide. The difference in surname spelling is due can be due to people writing what they think they hear or the fact that illiteracy was more prevalent in the mid 1800s than it is today.

Hope this helps.