....or is my Z not pulling like it used to? Let me give you a little background.
03 Touring 6MT 26k Miles. Completely STOCK.
Tranny replaced @17k along with clutch all courtesy of Nissan.
Getting locked out of 2nd and 3rd on occasion thinking it might be time for another tranny.
Loud Throw out bearing noise when clutch out in neutral(read up on it common problem but should not affect performance)
Hear a thudding from engine like knocking when taking off in 1st gear from a stop.
Clutch doesn't grab the gears and push you back in your seat like it used to. More like it just gently goes into gear but does not slip.
WOT used to really impress the $hit out of me... now it seems like it's holding back. Example. I was merging onto Hwy WOT 2nd gear and it was pulling decent but then @ 5.5k I got a power burst almost like turbos kicking in. Weird.
I don't know if it's all in my head or maybe something wrong. Maybe it's just time for some FI or a faster car. Any thoughts? Thanks!

 

You could just go get a simple tune up or a reflash and see how that works out for you... It also may be that you have just become sensitized to the feel of your car.

 

The '06 Z is calling you!

 

The clutch problems that you mentioned have nothing to do with engine performance. Get a dyno test.

 

Go test drive a 03 from a used car lot and do a back to back comparison.