First, I am not a benchrest or competition shooter and I am not a 1000 yard shooter. I do shoot at 500-600 yards a lot and my two longest game shots are 599 and 725.
A couple of questions and comments:
1) what are you defining as custom? Some folks think a factory gun with an upgrade to the barrel and a new stock is custom. Others think the action has to be "limited production" to be a custom.
2) What are you trying to achieve? a sub 1/2 moa gun or 1/2 to 3/4 moa gun?, You can regularly achieve a sub 3/4 moa gun with quality factory rifle and handloading or just an upgraded to the barrel and trigger as well as a bedding job.
3) Are you looking to do - hit a 1 moa target out to 1000 yards or just sub 1.5-2 MOA out 600-700 yards. The former likely warrants a $1200+ scope, the latter can be done with a $250-$700 scope.
4) I would focus your money in the following order - the barrel, scope, the trigger, the action (because a blue printed Rem 700 is a fine action), followed by the stock.
Money sometimes equals quality and sometimes it doesn't. Custom rifles have become the outdoor version of custom sports cars. People spend a ton of money on components building a car that their driving skills can't ever live up to, then want debate how their component selection is the best and much of their enthusiasm for their customized product is to rationalize their expensive endeavor. Kind a like a ~85ish golfer justifying his custom clubs.
The two most accurate hunting rifles I have owned both consistently sub 1/2 moa were blue printed 700s with douglas barrels.
The other think I would add is if you are contemplating a 100 yard rifle ask yourself how often are you going to access a 1000 yard range. Fore some it's twice a week, others twice a month, others twice a year.
Good luck and enjoy your project.