I've done lots of customizing and done two custom rifles.
First, settle on an action. Try Frank DeHaas's book, Bolt Action Rifles. I like the big four, Remington, Winchester, Sako and Ruger. For a big game rifle, I'd prefer either Ruger or Winchester. DeHaas's book will give you the strenths and weaknesses of all of them.
Select a barrel for it and send it to the barrel maker to have it fitted.
If you want nice wood, I hope you know somebody who does that kind of work if you don't. For me, I'd have to see the work and talk to the owners of the finished rifles. Getting a good, reliable rifle made with pretty wood is expensive and tough to do unless you can do the work yourself and know how to do it. But really dazzling wood can do for a rifle that nothing else can.
Frankly, I'd take a good look at some of the better rifles from makers like Kimber if I wanted pretty wood. Both Remington and Winchester have custom shops for this kind of need. Frankly, the fastest way to run up the cost of a custom gun up is to go with fancy wood.
I, too, much prefer quality synthetics. My synthetic stocked guns never change zero. Even if I remove the barreled action and put it back in the stock. Same zero, day after day.
Frankly, because the actions and barrels of today's rifles are so good, I'd buy a factory rifle, throw the stock away, and go from there. Particularly if I wanted fancy wood. Assuming of course that Kimber, Sako and the custom shops couldn't make me happy.
I'm also going to admit that my custom guns don't really shoot that much better than a well tweaked factory rifle. Tweaked means trigger job, or replacement, glass bedding and no cheap, moulded synthetic stocks. Maybe a new barrel crown, etc.
However, I got just what I wanted in specs on my custom rifles. Weight and lenth of barrel, stock dimentions, finishes, etc. The barrels clean up faster and stay cleaner. The rifles shoot different loads close to each other. And they are more accurate. It's lots of fun shooting groups that go down into the .2-.3's with light sporters. One to two inches will do, of course. Any decent factory rifle should do an inch or less with good ammo, or handloads, if properly setup.
So, would I do it again ? I'd make sure I couldn't find something that would satisfy me from one of the better makers. Then it would depend on what it was for. If wanted a really light, well balanced big game rifle, I'd do a Kimber Montana. But if I had to have a rifle with certain special characteristics, I'd probably go with another custom. Being a "rifle looney", I'd probably not be really happy/satisfied unless I did at least some customizing. E