If he was in the 9th Miss. at Guntown when he transferred to Woods, he would not show on the next 9th Miss. Regt. roster because the 9th along with the rest of Bragg's Army next mustered at Chattanooga and were gone from Miss. before the 14th of August 1862. He may have missed the previous roster because of the transfer being between muster dates.
The same holds for being "last paid" on a date prior to joining a unit. The "last paid" notation had nothing to do with what unit, but whether the man was owed any pay.
I can't speak to his 1863 "desertion" because I do not know the specific circumstances, but I can say that there were so many men deserting at that time, even the most die hard patriots knew that sometimes taking care of family or avoiding death from illness in the camps by deserting could be "forgiven" over time.