Joia --

You have much more information about this man than usually available. It will help to understand the process involved to produce these records.
http://ancestryinsider.blogspot.com/2008/12/compiled-military-service-records.html

Sometimes clerks made transcription mistakes. It's also important to know that original documents may contain conflicting and inconsistent entries. For that reason the record reporting McDonald's admission to the hospital at Liberty VA on Aug 6, 1863, is probably incorrect. Based on hospital rolls, the date should be 1862, not 1863. He appears on his company roll for Aug-Sept 1863 as present.

Reviewing McDonald's record, he enlisted in Lauderdale County on Oct 12, 1861. His company, the "Calhoun Guards", organized under Capt Edward A O'Neal on May 25, 1861, at Florence, AL. Officers and men entered Confederate service at Centre Star AL on June 3, 1861. They were sworn into service at Lynchburg VA, June 18, 1861. When the 9th Alabama Regiment organized at Richmond VA on June 26, 1861. O’Neal was appointed Major and 1st Lieutenant Dougle W. Gillis became Captain of Company "I".

One of the records shows McDonald as a member of Company "D". That's because a War Department clerk who transcribed McDonald's record wasn't sure whether the cursive letter on a hospital roll was the letter "D" or "I". Since he wasn't sure, he listed both letters. Of course we know from company rolls that McDonald belonged to Company "I".

To explain the record from the Alabama State Archives, it's different from the compiled service file at the National Archives. Before the end of the war, the Alabama State Legislature commissioned their own version of Confederate rolls for Alabama units. A commissioner was sent to Alabama regiments with a booklet form for each company. Company commanders were instructed to complete the booklet listing one line for every officer and enlisted man who ever belonged to the company. The form included residence, age and marital status of every member, including a notation for every battle or skirmish in which the member could have participated. Booklets distributed to this regiment were completed at the end of 1864.

As far as McDonald is concerned, the first company roll available at the National Archives for the 9th Alabama Regiment is May-June 1863. Dated June 30, 1863, Fayetteville PA, it shows him present. The ADAH roll shows that McDonald missed the Battle of Chancellorsville VA (May 2-5, 1863), so we can assume that he returned from his assignment at Liberty VA after the fighting ended.

The ADAH roll shows McDonald absent, sick, or absent on detail up until that time. New recruits often became sick shortly after arriving in camp and were absent for some time as a result. Looks as if this happened with McDonald, who was away from his company due to illness for most or all of 1862. He is present from the May-June 1863 roll through the last roll on file, Jan-Feb 1864. Clothing receipts for that period must have been issued while he was present with his company.

I hope this helps with some of your questions.