do i have to follow the running in progress which is keep below 7000rpm for the first 1000 miles?
my bikes done 450miles and the engine feels choppy or not as smooth as before, maybe im running it in to hard?
Not sure the breakin procedure for the R3, but you should vary the rpm often. The way I break in the bikes is I go on long rides, do little pulls then let the bike slow it self down. You can feel the engine change once it is broke in. Then change the oil once hit hit the break in mileage mark. If you do go above the 7000 mark, you should not stay there long. 7000 seems a little low to me. Is that what the manual says? What is your redline? You could always take it to the dealer if it feels weird and ask them if it is normal.
I agree with Legallyfast on the break-in. Vary the RPM's, maybe let the bike warm up and cool down (heat cycles) more often during break in. Try to follow the RPM limit and proper break in procedure recommended by the owners manual. I broke that RPM limit several times during break-in but didn't stay there for long.
I also notice some choppy engine feel on my bike, feels like the bike has very good compression going through the gears. I always assumed it was the fuel injection, carburetors seem so much smoother to me. Yamaha installed a progressive throttle twist on the R3 to remedy that choppy feeling, I'm sure it helps some but I still notice it.
Think the manual says "avoid prolonged operation above 7,000 rpm".
I tried to stay above 6,000 during break-in (very hard on these engines to "lug" them down). They're built to run at high rpm. Don't be afraid to take her to 10,000 or more momentarily - just don't cruise at 9,000 for ,more than 10 min.
Suppose it depends on your definition of "prolonged operation" is.
I prefer to break the rings in fast - few runs each from 3,000 to 6,000 WOT, then use engine braking to come back down.
Did 3-6,000, 3-8,000, 3-10,000. Important to use engine braking to help seat the rings. Baby it, and you could end up glazing the cylinders, and losing power = pull the jugs and rehone the cylinders + new rings.
Just my opinion, but worked for all my bikes including a KLR650, which are notorious for burning oil.