Yeah, I only provided info on the substitution question. Kalle provided information on the motion and eligibility question, but I will add some things.
As Kalle says, we really don't have enough information as to the exact positioning of the players, but, by your description it sounds like you started with 10 players on the line, and one in the backfield. And, it sounds like you sent one of those linemen in motion from the line. That's illegal motion. The only player that may be in motion at the snap is a BACK. To be a back, a player must be in the backfield and fully stopped before going in motion. And, of course, he, and the rest of the team, must comply with the "shift" rules, if he moves from the line into the backfield while another player(s) is(are) also moving (i.e., there must be a one-second pause AFTER all are fully stopped). The penalty for that is 5-yards from the previous spot, and repeat the down.
If he comes off the line from the interior of the line (as it sounds like he did, in this case), he is ineligible. So, when he touches the pass, that is also illegal touching by an originally ineligible player. The penalty for that foul is 5-yards from the previous spot PLUS loss of down.
The only players on the line that can be eligible are the players on the two ends of the line, and only if they are wearing eligible numbers (0-49, 80-99). All other linemen are interior linemen, and are ineligible (regardless of numbering). So, if you had thee players split out wide to the right, and all three are on the line, only the end can be an eligible player, and that is only if he is wearing an eligible number.
However, the opposing coach's complaint about an ineligible downfield on THAT specific down is not valid, because the pass did not cross the neutral zone. Ineligible players may be wherever they want to be if the pass does not cross the neutral zone.
