A 2/12 @ A35.

QB A11 drops back to pass. Running back A32 releases out of the backfield, crosses the line of scrimmage and is held by B51 before the ball is thrown. QB A11 throws the ball to A32 who; 1) catches the pass and is down at the A40, 2)misses the pass; incomplete, 3)the ball is uncatchable.

What is the result of each scenario. NCAA rules, down, distance, clock.

A hold against an eligible receiver on a pass that crosses the NZ is going to net an auto 1st down and 10 yards from the basic spot. ( you didn't say where the hold was)
Pass being uncatchable is not a factor.

Status of the clock depends on what caused it to stop. So in #1 it will be on the RFP and in #2 and #3 on the snap

In this case the Basic Spot is the Previous Spot

A 1+10 @ A45

a) ready
b+c) snap

It's important to note that the auto 1st down applies only if the pass crosses the NZ, but then it applies to all fouls against eligible receivers.

A 5 yard face mask on a receiver running a route would in this situation include a 1st down.