I bought this car recently and it went through a PPI at Honda without problem. The owner before my seller changed the clutch master cylinder and this car only had about 27k miles at the time it was done. Car now has 38k miles.

The noise as below

-Car running in neutral
-depress clutch pedal
-shift into gear- clunk noise(front end shakes a little, almost like pushing something in or out, as the car vibrates as the noise happens.)

This only happens when I depress the clutch pedal first then shift, no noise when shift back into neutral and reshift into gears.

Is this normal ?

 

Normal, my '05 does this, I'm wondering if it's the dreaded clutch delay valve that does this? Maybe someone else can confirm because I haven't removed my clutch delay valve yet but what you're experiencing is normal.

 

Not the clutch delay valve. If you depress the clutch, and wait a sec, then push into gear, it will not happen.

The reason, and reason if you do a do over by putting in neutral then putting in gear again it also doesn't happen...is that what is happening is all the shafts inside trans are all spinning at idle rpm, and when you push in clutch and immediately push into gear, all those shafts come to a halt, and that is what causes the thumb. If you do a do over the shafts are already stopped. If you pause a sec first, the shafts can spin down on their own.