Okay, after some research it sounds possible, My uncle says it sounds like it could be the clutch to him but he hasnt heard it either I was just describing it to him. I would upload a video but the ones my phone takes are the wrong media type to upload here. I got it to start off the key again the fuse for the clutch pedal position switch was blown.

 

Upload it to YouTube and copy the link

 

Here's a video I recorded of it at first you can hear the "whirring" sound when the clutch is let out it goes away when the clutch is pushed in, and later the grinding noise.
Thanks

 

Check the transmission fluid level. Those M5R2's are noted for leaking out the top 3 holes in the front of the tower. Clutch in the out position you are loading the transmission front input shaft. That's where I would start before ripping out the clutch.

 

AK Doggie, there's a fill and drain plug on the side of the trans where is the check? Does it have to be so far from the fill plug? Maybe I misread but you said clutch out is loading the transmission input shaft that's where I would start do you mean start by checking the oil?

 

The Transmission was low, so I added 1qt that's all I had around and it still isn't full (probably not a good sign) I also noticed that whirring sound is quieter if I slowly let the clutch out almost to the point where I cant hear it not sure if that could have anything related to the grinding or not but just thought i would mention it. I put the transfer case in Neutral and shifted through all the gears and 1-3 and Reverse are quiet (besides the whirring noise) and 4 and 5 I can hear the gears not sure how to describe it but there is some gear noise on them 2.