Hi Stephen,
I run into this all the time as I get requests and need either information from factories/vendors or need additional clarification from the person sending. What I do is draft a response in my email (so that the original request is in the email thread) and when I respond back I bcc my inbox email for my GTD system as it can receive emails and log them into the system. I add some notes about what I am waiting for and put it on my waiting list with the title matching my final action.
So for example just this morning I received a request to price up some mechanical equipment for a jobsite. My Next Action is to Submit Budget (I do not need a project as this is just 2 pieces of equipment so a simple budget). However, I am waiting for the factory to get back to me. I emailed the factory with a narrative of the request and bcc'd my system. When I clarify I change the title to Submit Budget for Mechanical Equipment for Project X. I mark it as waiting for and I create a tag for 3rd Party (so I dont have to have every vendor in my GTD system). I scan my waiting for list 2x a day so I will constantly be mindful of it. I have a notes section and I logged when I sent the request and when it is due.
When I receive the quote back, I can move this into my Next Actions, work on it, and complete the next action.