Delay on end line
 

Last night in Boy's JV game A1 is trying to throw the ball in along the endline after a made bucket, when B1 steps over the line in defending and the referee gives B1 a delay of game warning. He then hands the ball back to A1 to inbound and makes no visible indication whether it is a spot throw in or whether A1 can run the endline. When A1 starts to run the endline, the referee whistles him for a violation and gives the ball to team B.

First, the delay warning doesn't take away A1's right to run the endline, correct?
Second, it is proper mechanics to visibly note a spot throw in or indicate that
A1 can run the endline, correct?

Ouch.

Correct and correct.

Sounds like your partner kicked it into the third row.

You are correct it should not have been a spot throw-in.

7-5-7b A team retains the privilege if the scoring team commits a violation or common foul and the ensuing throw-in spot would have been on the end line.

It is a violation when 9-2-10 The opponent(s) of the thrower shall not have any part of his/her person through the inbounds side of the throw-in plane...The first violation shall result in a team warning for delay (unless a delay warning has been already issued to the team), the second will result in a technical foul (for any delay).