Keeping a Threaded Pipe at 90 degrees
Assuming that they are threaded in correctly, you just need to apply adequate force. Pipe threads are tapered to make a seal (which you don't care about in this application) but there is considerable latitude in how far they can be tightened, with proper pipe wrenches (always use two.)

Otherwise, you can add unions to get exactly the angle you want, but the normal approach (particularly when you don't have to make a seal) is just to get them tight enough, and then crank it up more to get them aligned. You have to really overdo it (or start cross-threaded) to seriously damage the threads.

You MIGHT find some benefit in using pipe dope (as for sealing) since it will provide some lubrication, without being all slippery like grease or oil. i.e. It's designed for the job at hand.