This is a complex question. The first response by most folks when you mention building a custom rifle is "You can buy a factory rifle for less money" and this is essentially true. But this presumes that you would be happy with a factory rifle and if that were true why would you be asking about a custom gun? If all you want is cost effective and serviceable then yes, go with the Win/Rem or whatever. But some guys want something different, unique or personalized.
You seem to want the Mauser action. Good choice IMO. I believe the bolt gun design has not been improved since 1898. You have three ways to go, as I see it.
1. Buy a factory Mauser like the CZ or Sako. But again, you could have done that without seeking suggestions on a custom gun.
2. Build one from scratch. A military action will require a lot of work to civilize. If you are into a truly elaborate project and don't mind the cost and effort then go for it. If you want to cut some corners, an alternative plan might be to start with a commercial Mauser 98 action. Pictured below is a rifle I built from a brand new commercial CZ action I got off GunBroker for $245. It came with the dual set triggers and I picked up a Douglas barrel that had been used some then taken off. Cost me $50.
I got the stock as a second from the Great American Gunstock Company (danged if I can find any flaws in it but it was priced at $125 for being below standard). Added a checkered steel buttplate for $25 (was going for the European Sporter look). Had a smith install the barrel, fit the semi-finished stock, then install the front ramp sight and barrel mounted sling swivel. He charged me $125 for all of this and it was a deal. I bagged a Redfield receiver sight off ebay for $15. I could scope it if I wished as the holes are there but I like this set up.
Total investment is $585. The barrel and action were blued as new, and all the necessary holes were already there as was a proper safety. All of this would require attention if building a military action and would add to the cost.
What do you think? I think it beats an off the shelf Ruger or Remington hands down.
3. The remaining option is buy someone else's project and make it your own. Half-finished custom rifles can be found cheap. Even completed custom guns can be bought for less than the sum of the parts. Everyone always says you never get your money back when you sell a custom gun but that's good if you are the buyer! I regularly peruse the GunBroker auctions looking for unfinished projects that the owners have given up on and are selling cheap.