Yes, it is possible (and allowable) but this is going to be a large project. You wrote, "finding all the data on the 6th is not easy". Amen to that!
Copies vary in quality because over time different people have made copies for you, and they are probably using different types of copiers.
If you really want to see all the records, here's my suggestion. Get the microfilm. Stone's 6th Texas Cavalry appears on reels 37-42 of M323, Compiled Service Records of Confederate Soldiers Who Served in Organizations From the State of Texas. This will cost about $250 for all six reels; in other words, about a tank of gas per reel.
Ordering from a Mormon family life center (Church of Jesus Christ of Latter Day Saints) will be less expensive. The other alternative would be to check catalogues of nearby libraries for M323. If they don't have it, you can order microfilm through their interlibrary loan process. In any case, you'll need access to a microfilm reader.
If you plan to transcribe or abstract all the records from a particular command, study a reasonable sample of the records first. You'll begin to see patterns repeated in different types of records. Once you decide how to deal with these, it will make the entire process easier.
Access to a reliable laptop computer and software like Word or Excel will help tremendously.
Feel free to ask other questions about the process.