I'm a little confused on this question.

While A-1 is in the act of shooting, A-2 fouls B-2. Ball enters basket. Is it a good hoop?

If the ball had left A1's hands, yes...otherwise, no.

...and if you're not in the bonus yet, B gets the ball under A's basket with running privileges. Which confuses the heck out of coach B, because it looks as though there is no penalty for team A. My personal opinion is that team A should lose the basket no matter where in the process the ball is. But I'm too busy with my real life to start e-mailing the NFHS, and making a stink. Coach B is just going to have to get over it!

Is this correct under NFHS 7-5 article 5
after a player control foul or after a common foul prior to the bonus...... make a throw in from the designated out of bounds spot nearest the foul.

I read it as a spot throw in
stew in VA
CVBOA

I assumed the shot had not left the shooters hand- if the shot had left the shooters hand and the basket went in- yes you would have running previleges
stew in Va
CVBOA

Yes the Casebook play is 4-19-2. If the shot is successful Team B gets the ball on the endline and can run.