I see nothing wrong with installing a new turbo while doing head gaskets before building the transmission. In an ideal world, sure, build the transmision first, but blown head gaskets aren't an ideal world. It will be much easier to swap the turbo while the heads are off. No reason the stock transmission can't live a long life as long as the tuning is kept very mild. Then he can upgrade the transmission when funds are built back up.
I think Tony at All Season Diesel has a water pump that is supposed to be modified to prevent the gear and impeller from spinning off. You might want to talk to him about that. The standard ARP head studs will work just fine for what you are wanting to do. The new LML style head gaskets are holding up very well from what I hear, and they are quite a bit less expensive than the previous versions to boot.
You already have some good suggestions on upgrades. I would probably do the EGR delete and maybe even a high flow intake bridge. An aftermarket intercooler might not be a bad idea since the stockers are prone to leaking. I would also consider upgrading injectors while you have it apart.