- After some correspondence with marstar, it appears that the PTRD is a controlled good, so I need to be registered with them (controlled goods, not Marstar, if I can

) before I can get one
I would recommend checking with DCG yourself. As i've said before, i know people with these rifles who are not registered with DCG.
- I have a friend who is a machinist, so I might be able to get deals on custom cases
You should be carful as CanAm said.
Now some questions:
- if the ammo is a controlled good, would it be legal to make?
Look above
- Where could I get bullets (cast?)
Launching a cast bullet at 1000m/s is a bad idea. Its much better to turn bullets on a lathe from brass.
- what powder would I use?
This depends on a bullet. Most .50 bmg powders should work
- i could use .50 bmg primers if make the cases as such, right?
Yes
- what would I need for a backstop when I'm out shooting?
A mountain.. a big one..
- are tracer rounds legal?
Yes, but good luck finding 14.5mm tracer bullets