Only while moving. I can rev all the way up to red line with the clutch in while sitting still and there are no vibrations. Only while moving. And only when my RPM's would be high if I were to let out my clutch.

 

Then I don't see it being the clutch or clutch related, you would hear it all the time. Ok, how about when standing still, with the trans in neutral, and the clutch engaged to get the internals spinning. Then if you pop in the clutch and fiddle with the gears, will it do anything?

 

No. Only while moving, does it make any vibrations. Like I said before, it seems to be doing it if the motor were to be at high RPM's if I were to let the clutch out. So 2nd gear vibrates with the clutch in cruising at 35+... 3rd vibrates with the clutch in cruising at 60+... It also vibrates with the clutch out but what bugs me is that it does it with the clutch in too. I was thinking maybe the input shaft is bent?...

 

Could be the input bearing or even the counter gear shaft bearings. Sure sounds like you have some play in that area.
If it is the input shaft bearing or counter gears you should really feel it in the shifter way more then any place else. I use to tell the differents between a failing input shaft and throwout bearing with the feel of the shifter vs the feel of the clutch pedal. If your feeling it in the seat of you pants then I would look more to the driveshaft issue Camaro69 described. He is right even a small twisting of the motor could change where the motor is resting. If there is not enough clearance it would cause a vibration that could feel about the same on the floor and the shifter.

 

I just remembered an issue we had walk in once were the transmission bolts had come loose. Caused al kinds of odd vibrations. It was real bad on down shifting. You may want to check the bolts between the Tranny and the bell housing and the bell housing to engine bolts. I guess it all depends how bad the vibration is.

 

In the attachment, which part is the input shaft bearing? If you are referring to 33 or 34, those are:

(33) Case Extension Bushing
(34) Case Extension Oil Seal Assembly (Model Dependent)

 

1) What you're showing in the pic is an automatic, he has a manny tranny (T5)
2) The input shaft is at the front of the trans, you're referencing the output, at the rear.

 

Thats a 4l60E, he has a t5

See circled area. The bearings are the ones with red dashes.

 

Thanks guys. I noticed that you don't feel it as much as you hear it. It sounds like a fan spinning when it's missing a blade. Or like a phone vibrating lol. But I only feel it in the shifter and barely in the floorboard. Mostly in the shifter.
I checked all of the transmission bolts and they're all tight as can be. I'm thinking I have a bad bearing... It seems like there's some play in the input shaft. That's exactly how I would explain how it sounds like.

 

Probably a bad bearing. If there was play it would leak. Does your trans leave any fluid on the ground?