I recently had a gearbox which went through the casing and needed to be refurbished. Had a new clutch replaced along with it. Once i picked the car up i began noticing that when the car goes into 2nd gear the car throttle will not accelerate the car and the engine will not rev even when i press it. This would only happen in second gear(this seems to also be very random and not a constantly occurrence) and to get the car accelerating again i have a choice of either pressing on the clutch pedal (whilst its engaged in 2nd gear) and the car will suddenly regain power or change into any other gear. I have before accelerated up to 5k revs on second gear and around 4-5k the acceleration would completely disengage and i'd have to change gears.
I went back under warranty to the mechanics and they took the car into Volkswagen specialist which came out with codes that the car is running lean (I have cat back exhaust, k&n filter) however this problem wasnt occouring before the broken gearbox and even during commute with the broken gearbox to the mechanics. Any help is much appreciated as i need to start narrowing possible causes for this, mechanical or electrical