I have a 2004 yamaha YZF-R1,when I start my bike in neutral and go to put it in first gear my bike dies.After I start the bike I pull in the clutch and downshift Into first gear from neutral and it just shuts itself off completely. What is wrong with it or what am I doing wrong???

If your side stand is not down or you already have your sidestand bypast and your bike still has this problem as mine did also the problem is located inside the main relay master relay what ever you wanna call the big one under the seat. if you take a knife or razor blade get it real hot with small torch and carefully cut the back off it you will find the there is like 5 diodes inside and the middle one is either broken or deffective you can test it befor you cut it open with a tester its in the manual how to test it but i cut mine open and it was broken in half. took me a month to figer it out but 1 guy on web posted about it and sure enough bam there it was

Your kickstand is still down

Hello,
I dont think that you are doing anything wrong. Your bike has a side stand safety switch. the switch is designed to cut the engine if you put it in gear while the side stand is down or it thinks that the side stand is down. There is also a clutch lever switch that allow you to start the bike in gear while the clutch is pulled in. I would check the side stand switch first and make sure that the side stand is lifting all the way when you flip it up. If the stand is bent or dry, corroded it may not be activating the switch properly.
Next you should check the clutch lever switch. Make sure that the connector is plugged in properly. Also look underneath the lever and you can check the plunger for the switch to make sure it is moving freely.

If you have recently added different levers or a sidestand this can be the problem. somne of the aftermarket parts have to be worked on in order to get the switches acting properly.

Thanks and I hope that this helps.
Steve