Just a thought, I saw you mentioned water pump for reliability. I presume this is a build on an older car with high miles? I thought about the same thing on my SVTF when it comes time to either overhaul or buy a new car.
If I were doing a full engine build, I personally would replace EVERYTHING possible. All pulleys, tensioners, etc on both the timing belt and accessory belt. Water pump for sure.
I had a shop do my timing belt & clutch. I gladly paid for all the pulleys and tensioners and water pump. Those parts are cheap, stupid cheap, and there's no reason not to replace them if your into the build that deep. It'd be a shame to do such a monumental build and have a timing belt failure caused by a $25 pulley or tensioner that failed. It's rarely an issue of the belt physically breaking. For most timing belt failures the belt may have been fine until a pulley failed.
I'd consider checking all hoses, both for coolant and vacuum. It will save you headaches later. Stupid little things can be annoying, like the rubber hose on the PCV valve is stupidly close to the exhaust manifold, it dry rots easily.
You may as well change all the little crap like that to ensure you don't have to try and chase down something annoying like a vacuum leak while trying to tune a newly built and turboed engine. I know you mentioned a PCV delete, but just using that as an example. Rubber hoses on 9-11 year old cars could definitely use refreshing if you're building up an engine!
As far as axles handling the torque, or heads flowing enough for 350+ hp, I don't have the expertise to address. But wanted to wish you best of luck with the build!
And when you get it done I'd consider a trip to Reading to see it and buy ya a beer for a chance to ride shotgun and see if I want to spend this kind of money on my SVTF down the line.