So a little clarification. A lower is either a pistol or a rifle, it will never be classified at purchase as an SBR. While you may buy the gun as an SBR direct from an FFL, the lower at that point is still considered a rifle (Short Barreled
Rifle), just that you have the requisite Form 1 (or 4) to posses it in a shorten configuration.
As to your question, you can do several things.
1.) Purchase the lower as a pistol, take it home, slap an upper on it less than 16" and shoot it as a pistol until the Form 1 clears (engraving can be done before or after you get the stamp), then install your stock and you're good to go. The benefit here is that you can go ahead and buy the upper you want and start playing around with it to make sure everything works.
2.) Purchase the lower as a rifle, take it home, put a stock on it, and wait to purchase a short upper.
There may be a third or fourth conceivable option, but beyond these two it just gets too convoluted.
My suggestion would be to go with #1. The reason(s) I say this are, as someone else pointed out, a pistol can always be made into a rifle (and back again), but a rifle can never be made into a pistol. Second, by going this route it allows you to start tweaking the gun before the stamp shows up. Yes, it won't be exactly the same without a stock, but you can check it for function and do any modes you want to while you wait.
As to the points about not purchasing the stock until you get the stamp etc., if the only lower you have in the safe is a rifle lower, and the only upper you have is a short upper, then it wouldn't be too hard to prove constructive intent. However, if you've got other ARs, who's to say that the stock isn't to swap on to one of them? I think a lot of folks get really worked up over this without considering the whole picture. Conversely, once you have one SBR'd lower, you can have as many short uppers for it as you want, so constructive intent becomes even less of an issue. By going the pistol route (as stated above), you're pretty well insulating yourself from 99% of the issues that someone could potentially run into.
Edited to add:
So for a little explanation on how you can do this without running afoul of the law, see what I did below. We'll focus on guns #2 & 3 (top to bottom) in the picture below.
Order of purchase/build:
-Lower on #3 was set up as a pistol
-Upper on #2 (11.5" 5.56) was purchased and placed on lower #3
-Lower #2 was purchased as a rifle and immediate filed Form 1 on it for SBR.
-Once Form 1 was approved, upper #2 was swapped to lower #2 (now an SBR).
-Lower #3 converted to rifle with addition of stock.
-Upper #3 purchased (8.5" 300 BLK), was left in the safe with the now SBR rifle #2. (As I said, you can have as many uppers for an SBR'd lower as you want).
-Form 1 filed for lower #3
-Form 1 approved, upper #3 put onto lower #3.
