So I recently replaced my stock clutch with a stage 3 action clutch since I’m planning on adding more power, but after a couple of days it started making a weird sound. It sounds like when the window motor is trying to send the window up but makes like a struggling sound. I don’t know if it’s the fly wheel or the throw out bearing.

 

It has been many many years since I replaced a clutch on my 55 Chevy but the job consisted of a new clutch disc, a new pressure plate, and a throw-out bearing.
Why have you not done the same?
FWIW from what I understand Infiniti's do not play well with aftermarket parts.
On my previous 06 G35 6 speed it still had the original clutch when I traded it in at 171796 miles
A properly driven manual shift vehicle should see 200k miles before a clutch replacement is needed

 

It came as a kit so I replaced clutch, pressure plate, and bearing. So I replaced all three not just the clutch disc

 

More information required. When does the sound happen, does it ever NOT happen, video of noise, etc

 

Record a video and post it to facebook, then post the link here and it will embed the video automatically.

Trying to describe something like this is nearly impossible.

For the future, when you replace the clutch you do the flywheel, throwout bearing, the master and slave cylinder, and all the fluid.

Did you reuse the flywheel? God I hope not lol.