A1 is going to shoot the free throw. The lead official does not notice that A2 is in the "bottom spot". The lead official bounces the ball to the shooter. After A1 gets the ball, A2 and B5 switch places. It caught the officials offguard. A1 releases the ball without the officials signaling yet for the violation. (Wait, I'm not done yet!) B4, who is in a legal spot, enters the lane too early. What do we have?????

Double violation on A1 and B5.
Shoot the next one, or go to the arrow.
Forget B4 because violation occured after the double.

I'll give this one a shot since I am being snowed in by at least 18 inches of snow and our basketball tournament is canceled today.
NFHS
Best case would be for Lead to notice wrong player in lane space before ball is at disposal, and tell them to switch.
BUT, since that didn't happen, there should have been a whistle for double violation as soon as A1 had ball in hands. No shot, go to AP if there is not a second shot coming. And since THAT didn't happen, there should have definitely been a whistle for the double violation as soon as the two switched places while A1 had the ball (this was very helpful to the refs as it made thing obvious). No shot, AP arrow unless second shot coming.

Since the refs seem to be sleeping during these violations, perhaps they "missed" B4 going into the lane early, also.
If they penalize this violation, I guess they just have to go with it (as if the original violations had not occured).
Sounds messy. (Little kids in rec ball, maybe just get them lined up correctly and start over?)

Will this stuff melt in time for baseball season?

DOH!!! I hate when that happens. :-)

I agree. Even if they don't switch the book states that A member of the non shooting must be in the bottom space. B violates by not being there, and A violates by being there.

The thing you need to do is get into a habit of checking that the two rebounders on the bottom are not on the same team as the shooter. What I do is say the color of the uniform of the two players on the bottom to myself, then look at the shooter and say his uniform color to myself. If the rebounders are the same as the shooter I know I have a problem. This takes about 1 second and has saved me that problem many times.

Blackhawk

On page 61 of the Case Book, Rule 9.1 Comment, it says that a team forfeits its right to any space not occupied before the free throw starts (when the ball is at the disposal of the free thrower).

Does this change anyone's mind on this situation?

Nope.
That rule does not mean the first spot may be occupied by the wrong team, it just means that once the shooter has it then he gets another shot if he misses.