I was thinking .243 with a longer barrel, and then you wouldn't have to go with such a heavy chassis system to offset recoil. You could get a McMillan style hunting stock sense it's going to be used for that too. Take my advice for what it's worth as I'm fairly new to long range shooting, but I've hunted all my life (lots of whitetail). You mentioned being from the south, so I'm assuming you're not planning on using this to shoot elk, so .243 works. I"m not sure what game animal in the south he would need to shoot from 600 yards. Most whitetail are shot within 150 yards. Also, take into consideration some advice I was given when looking into my first build. I wanted something that I could take elk hunting in wyoming and also use for long range shooting. Basically, you can't really have it both ways. For $3500 you're either going to get a really bad-ass long range/1000 yard rifle or a really bad-ass hunting rifle that does have the ability to reach out to longer ranges but isn't the "best" long range caliber. If you try to get 1 rifle that does both you're going to end up short-changing yourself on both ends. I know you're wanting to do something really special that will last a lifetime, hence the $3500 price tag. If it were me, I would start with maybe a $2000 hunting rifle that does have some ability at long range shooting, but focused mainly on hunting. In this instance a .243 or .260. Let your son learn on that for a few years and figure out what he likes and doesn't like. He can still take that rifle out to 1000 yards, it's just not optimal. Then after a few years, the two of you go in "together" on a long range build. Over the next 3 years I'm sure your boy could earn at least $1500 - $2000 doing some type of work, mowing yards or working on a ranch/farm (I made about $1000 - $1500 a summer mowing yards at 12, 13, 14). That's 3 yards at $25 per week, so $75 a week for 3 months putting him at $1200. Then you each put in $2000 and get a dedicated long range rifle. If he's 14 years old, he'll be able to handle a long action easier than he could today, and that will open up his options to a plethora of long range catridges.
Edit to Add: I guarantee you, your son will cherish both rifles, especially the one he bought with his dad that he earned.