mechanics

[Navcom]

A2/10@A-35 previous play was an INC pass,  A substitutes with 0:32 on the PC,  B begins its response (PC-0:29). There are 12 players in formation for B (PC-0:22).  The ball is snapped with 12 men in formation (PC-0:14) and A2 runs up the middle and is tackled at the A-43 Ruling, Clock?  Correct Mechanics?

A4/5@B-30 late in the 2nd quarter with no TOs remaining for either team. A2s FG attempt is blocked behind the LOS. Holder A1 recovers the grounded ball at the B-36 and frantically throws a forward pass to A-88 who was eligible by position at the snap.   A88 catches the pass beyond the LOS and is tackled at the B-22. The clock reads 0:02. Ruling? Clock? Options?

[dammitbobby]

I'll take a stab.

3-5-3b
Team B is allowed to briefly retain more than 11 players on the field to anticipate the offensive formation, but it may not have more than 11 players in its formation if the snap is imminent. Whether the snap is imminent or has just occurred, the officials shall stop the action. (A.R. 3-5-3-IV)
PENALTY [a-b]—Dead-ball foul. Five yards at the succeeding spot. 
3-5-3cIf officials do not detect the excessive number of players until during the down or after the down is over, or if Team B players have entered the field just before the snap but have not been in the formation, the infraction is treated as a live-ball foul. (A.R. 3-5-3-V-VI)
PENALTY—Live-ball foul. Five yards at the previous spot. 

 For both scenarios, 2/15 at A30.  Clock was stopped, so play resumes on the snap, 25 PC on R's signal.

second one:
by rule, A1 is allowed to recover and advance the ball (and therefore can pass the ball)
3-3-1a
ARTICLE 1. a. A scrimmage kick that fails to cross the neutral zone continues in play. All players may catch or recover the ball behind the neutral zone and
advance it (A.R. 6-3-1-I-III).

So unless I'm missing something, since it was recovered 6 yards behind the LOS, this is a legal play.  Clock stops momentarily for chains to reset, but since there is less than 3 seconds, rule 3-2-5 comes into play, which says that with two or less seconds on the clock, spiking to preserve clock is not allowed, therefore game is over.
ARTICLE 5. If the game clock is stopped and will start on the referee’s signal with three or more seconds remaining in the quarter, the offense may reasonably expect to throw the ball directly to the ground (Rule 7-3-2-f) and have enough time for another play. With two seconds or one second on the game clock there is enough time for only one play. (A.R. 3-2-5-I)

[ElvisLives]

A2/10@A-35 previous play was an INC pass,  A substitutes with 0:32 on the PC,  B begins its response (PC-0:29). There are 12 players in formation for B (PC-0:22).  The ball is snapped with 12 men in formation (PC-0:14) and A2 runs up the middle and is tackled at the A-43 Ruling, Clock?  Correct Mechanics?
——————————————-

Was B given full opportunity to get substitutes into position, and get replaced players off the field? There is no specific amount of time for this to take place - just judgment by the R as to whether B had full opportunity. If so, then you simply have a live-ball substitution foul by B, 5-yard penalty from the previous spot, repeat the down, for A, 2/5, A-40, or A, 3/2, A-43 (penalty declined). Gotta get the coach’s choice. In either case, the game clock will next start on the referee’s signal, and the play clock is set to 25 seconds and will start on the referee’s signal.
As for mechanics, the R (and other appropriate officials) use the “iron cross” signal until B has had full opportunity to get subs into place and replaced players off the field. Once B has had their opportunity, the signal is discontinued, even if B has more than 11 on the field (the R won’t know this - the deep official are responsible for the count of B players.  There is nothing more to do mechanically, other than to flag the substitution foul, if B still has more than 11 on the field at the snap.

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A4/5@B-30 late in the 2nd quarter with no TOs remaining for either team. A2s FG attempt is blocked behind the LOS. Holder A1 recovers the grounded ball at the B-36 and frantically throws a forward pass to A-88 who was eligible by position at the snap.   A88 catches the pass beyond the LOS and is tackled at the B-22. The clock reads 0:02. Ruling? Clock? Options?
———————————

This is tricky. The statement does not indicate if the holder is still ‘grounded’ when he recovers the ball, or if there is still a potential kicker in place to make a kick. If the kicker is still in a position to possibly kick the ball, or if A1 is ‘on his feet,’ then the ball remains alive, and the pass/catch/run results in a first down for A (1/10, B-22).
However, if the kicker was not truly in position to kick the ball, and A1 had some body part other than a hand or foot touching the ground when he possessed the kicked ball, then the ball is dead when possessed by A1, resulting in B’s ball, 1/10 (B, 1/10, B-36).
In either case, due to the legal kick down, the game clock will next start on the snap (regardless of which team will snap the ball), and, for the same reason, the play clock is set to 25 seconds and will start on the referee’s signal.

[ElvisLives]

I'll take a stab.

3-5-3b
Team B is allowed to briefly retain more than 11 players on the field to anticipate the offensive formation, but it may not have more than 11 players in its formation if the snap is imminent. Whether the snap is imminent or has just occurred, the officials shall stop the action. (A.R. 3-5-3-IV)
PENALTY [a-b]—Dead-ball foul. Five yards at the succeeding spot. 
3-5-3cIf officials do not detect the excessive number of players until during the down or after the down is over, or if Team B players have entered the field just before the snap but have not been in the formation, the infraction is treated as a live-ball foul. (A.R. 3-5-3-V-VI)
PENALTY—Live-ball foul. Five yards at the previous spot. 

 For both scenarios, 2/15 at A30.  Clock was stopped, so play resumes on the snap, 25 PC on R's signal.

second one:
by rule, A1 is allowed to recover and advance the ball (and therefore can pass the ball)
3-3-1a
ARTICLE 1. a. A scrimmage kick that fails to cross the neutral zone continues in play. All players may catch or recover the ball behind the neutral zone and
advance it (A.R. 6-3-1-I-III).

So unless I'm missing something, since it was recovered 6 yards behind the LOS, this is a legal play.  Clock stops momentarily for chains to reset, but since there is less than 3 seconds, rule 3-2-5 comes into play, which says that with two or less seconds on the clock, spiking to preserve clock is not allowed, therefore game is over.
ARTICLE 5. If the game clock is stopped and will start on the referee’s signal with three or more seconds remaining in the quarter, the offense may reasonably expect to throw the ball directly to the ground (Rule 7-3-2-f) and have enough time for another play. With two seconds or one second on the game clock there is enough time for only one play. (A.R. 3-2-5-I)

Which book are you using? Looks like 2019.

This was a legal kick down, so the clock next starts on the snap, by rule. There is no issue about spiking the ball.

[dammitbobby]

Yes, 2019 was the one I had pulled up. 

And I derped on the first one, and enforced the penalty against A, should have been walked off the other way.  I'm a very visual person and I struggle to 'see' plays described with words.

[ElvisLives]

Yes, 2019 was the one I had pulled up.
As you can see, it would make a huge difference in this case. By 2019, we'd have interrupted the game to enforce the substitution foul against B. But, by current rule, we allow the snap to happen and the down to run its natural course, and complete the penalty after the down. 

And I derped on the first one, and enforced the penalty against A, should have been walked off the other way.  I'm a very visual person and I struggle to 'see' plays described with words.
I, too, have been known to misread the statement. The lesson from this is to slow down, including on the field, and make sure of everything before committing to a final ruling.