R1 gearbox dont hav 5 gear on my 2006 r1 grinding noises only in 5th?

Pull the gear box drain plug and check for heavy metal stuck to the magnet. I suspect that the clutch in-put shaft bearing has failed. If so you will have to have the gear box rebuilt as the metal will have affected the other bearings

I suspect that there is a failed bearing on the output shaft or on the cluster shaft. This comes from the burnt oil condition which happens when a bearing is over heating due to failure and the gears not aligned when trying to change gears.

Sounds like the thrust bearing is worn to the bleep. Though I suspect it's not Synchromeshing. Some part of the Clutch mechanism failing critically.
See http://en.wikipedia.org/wiki/Manual_transmission#Synchromesh
http://en.wikipedia.org/wiki/Clutch
Did it run out of Oil? BUT then maybe damage has been done to both the internal of the Gearbox as well as the clutch, so yeah STOP driving it before more damage that can set you back a fortune

yes the syncro on 5th is gone.... its no major problem just annoying... you can get it fixed at a garage but i will say now it wont be cheap... if you have the revs at about 3000 when you change gear it will be minimal grinding ... cheers hope this helps

this sounds like a bearing in the gear box on the lay shaft maybe prop the bike up on a satnd and run it up in gear to here the gear box working
ps,,,dont let it fall off the stand when its running up!

driving along in 5th gear but then after about 30 seconds it pops out of gear and i have to put it back into 4th coz it wont go back into 5th.

No good news on this one I think
Your whining sound problem is the Layshaft bearings in the gearbox are badly worn. It also seems that the baulk rings are damaged on 5th gear.
John

sounds like syncro bearings in trans

Get a new one froma reliable source. It may be a 5 speed gearbox but it sounds like the synchros are gone on that one.

5th gear is gone, it'll be cheaper to find a good second hand one with a waranty than to get your one fixed sorry to say. The inside of gearboxes are only a place for gearbox specialists and they arent cheap unless you know someone.