I've read through all the threads on the marble in a blender and coffee grinder threads and I don't think this is the same issue. I'm hoping someone can shed some light on the issue. I've brought it in twice and my dealer hasn't been able to find the problem.

Sometimes when my car is in 3rd, 4th, and 6th gear. I hear one or two loud clicking sounds coming from underneath the gearbox right when I pass 3.5k RPM. When my hand is on the gear shift, I can actually feel the gear shift move/click forward as the sound is emitted. When I force the stick back against the gearbox, I can feel it suddenly forced forward just a slit bit.

The click is very specifically timed at the following RPMs:
3rd gear: 4k RPM exactly
4th gear: ~3.9k RPM exactly
6th gear: 3.5k RPM exactly.

When I go over these RPMs, the click no longer appears and there are no other sounds under these RPMS. But I maintain the engine around these RPMs, the click comes and goes right as it moves between the specific speeds. This doesn't always happen and only appears maybe 1 out of 3 times when I'm driving. Here are the details on my car:
1) Completely stock 2004, GT 6-MT, 58k miles. Bought it 1 month after release
2) Use 91 Octane gas always
3) Dealer serviced with dealer recommended oils
4) Infrequently red-lined
5) Engined flooded once in 2005
6) Sound started to appear about a year ago
7) Dealer 'tuned-up' the gearbox a bit around the same time the click started when I told them, the 3rd gear was hard to shift into sometimes.
8) Dealer couldn't find any problems.
9) Sound only appears when the car is in gear. If the car isn't in gear or if the clutch is pressed in while driving, the clicking does not appear.

I'm at my wit's end and about to take it to an independent mechanic to see if they can figure it out. My guess is that there's something wrong in the gearbox itself after the tune up and something wasn't screwed in right. Also worried it could be the engine itself. But given that the clicking only appears when the car is in gear and the clutch isn't pressed in, I'm leaning towards gearbox.

Any thoughts?

 

Are you sure it's coming from the gearbox?

The engine opens some auxillary ports to give it more air around that RPM and it makes a click sound much like the one you are describing. Drive with the windows down and see if you can tell if it is actually coming from the engine.

 

^ Beat me to it Could be the port opening and the movement of the shifter could simply be from the increased torque.. Could you post a vid or something?