Let's say I'm a dingbat and started to query while I was still editing my manuscript. Even with submitting queries via email, I thought it would take several weeks to hear back from anyone. (Everyone writer I know complains about how long it takes to get a response to a query so I thought I was safe.)
But, amazingly, I got a response the next day, requesting a full manuscript. What do I do?
Do I tell them it will be a few weeks before I get back to them? Or do I not say anything and send it when it's ready? Is this going to be a problem? Have I totally wrecked my chances with them?
First off, everyone learn from this writer's mistake. Do not send a query until your novel is ready to go—written, edited and as good as you can make it. (This is not an issue with non-fiction, as those queries are often sent before the book is finished.)
The good news is that unless whomever you sent it to was brand new and desperate for reads, they are either very efficient or you simply got in on the day they were clearing through their query file and sending out responses. Chances are they aren't sitting there tapping their foot, waiting for your full. However, if your query was so awesome that they really, really want to read your mss, they might possibly be wondering what's taking you so long. (I've had a few mss that I was excited to see. I bugged my assistant every day, asking if they had come yet.)
The other good news is your query was probably really good. Really good queries and really bad queries typically get fast responses, while those queries that fall in between take some time to think about. If your mss was good enough to want today, it will be good enough to want in a few weeks—probably.
The bad news is that the longer you wait to submit the full, the higher the reading pile will be on top of it and there's a possibility that someone else will send in something similar to yours and beat you to the punch.
If you can get it done in two weeks, I wouldn't bother responding. I'd just buckle down, work really hard, and do whatever it takes to get that mss finished and off (even if it means taking time off work and neglecting the family). If it's going to take you longer than that, I'd send a very short email (just a few sentences) explaining the situation and letting them know you'll send it as soon as it's ready.