I have a 2001 yamaha yzf r1 andwhen I start it up and it's cold when I shift the bikes shifts hard and the bike jerks forward then when it warms up I have problems shifting and if I can get it in neutral it then will not go back into first I can stand on the shifter and it won't shift

SOURCE: Possible blown fuse in 2002 Yamaha YZF R1

the fuse box is under neath the left side cover as in on the left side when you are setting on the bike it is the fuse that says signals i beleive it is a 15 amp fuse.

SOURCE: yzf r1 03 gear prob or?!

Sounds like bent shifting fork which is expensive. If you are not the 1st owner then you don't know how previous owner treated bike. Often sportbikes are rode hard and banged into 2nd gear which can eventually cause tranny problems like bent shifter fork. First look down by the shifter pedal and inspect that it is fastened securely to the shift rod coming out of the engine/trans case. There is a single bolt that holds the shift lever on a splined shaft and can come loose and cause problems.
If that is ok then find a local mechanic you trust....Good Luck !

SOURCE: 2001 yamaha yzfr1 shifting problems

You have a bent shift fork.
You will need an impact driver, flywheel puller, case splitter and torque wrench plus the normal screwdriver, pliers, etc.. Alternate to the special tools is taking it to the dealer and say "Fix it". I often tell people to take it to the shop just so they don't get into such an involved project.

The motor comes out of the bike then turned upside down for removal of the bottom case. The clutch, shift shaft, flywheel, electrics, gears and gear shafts gotta come out so you can get to the bad fork. There's much more but the idea is that you are better off having the shop do the repair unless you have experience, are extremely mechanically inclined, and have the tools. The bad news is that a shop is going to charge around $1500 for the repair. Some shop mechanics also repair bikes at home. If you find one, you can save $200 to $400 or so.

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SOURCE: sidestand and neutral light problem for 2005 yamaha R1

Try checking the wiring for snags or earthing out and test the side stand unit off the bike with a conductivity meter ..also try an oil change .

SOURCE: ineed a wiring diagram for 2008 yamaha yzf r1

http://www.yamaha-motor-europe.com/community/service/manuals.jsp