Thanks a bunch for your help, George. Sorry for the slow reply. I was hoping for a quicker response from the church, but still haven't heard anything. The grave marker is not of the "official" VA variety. Looks like someone had a monument shop create something. I just fear it's incorrect.
Again, I feel fairly certain that my Great grandfather is the John W. Ellis listed in Co. G of the 41st Mississippi. His service record cards indicate Co. G and that he enlisted in Meridian, Miss., which is near where he lived. I think I understand what you were saying about companies being organized in various locations and then forming with their designated regiment in a central location, but according to what I see online, the 41st regiment was formed in Pontotoc, Miss., about 150 miles from my ancestor's home and Company G was formed in Monroe County, which is not too far from Pontotoc, but is over 100 miles from where he lived and where the service record cards say he enlisted.
Would it have been uncommon for a company to be organized in one location and then perhaps the organizers traveled to other locations to "flesh-out" the roster? I'd be interested to see if there's a list of the entire Company G showing where each was actually from.