Vibration at 3200rpms 06 Mustang gt manual

I have a slight vibration at 3200rpms, most noticeable in 3rd and 4th gears. It's not present while reving the engine in nuetral. I tried removing my drive belt, but the vibration was still there. I had 4.10 gears installed recently hoping it would atleast move the vibration in the rpm range, but it didn't change a thing. I also have an aftermarket 1 piece driveshaft which just made the vibration more noticeable so I put the stock shaft back in. I think I can safely rule out the driveshaft and i've read that rpm specific vibrations are usually engine related anyway. I have a feeling if I take it to the dealer they will say it's a normal characteristic of the car, but i'm sure that isn't true. Any thoughts? I have an intake and custom tune for the car, so I put the stock tune and intake back on just to rule it out, vibration still present. Thanks. My next test will be removing the driveshaft from the transmission and running it up to 3200rpms in 3rd, if the vibration is still there, then i'll know for sure it's nothing aft of the tranny.