I have an "03" 400ex. My stock engine ran fine just had a little valve tapping. I then blew the piston to pieces. I got all the pieces out of the motor block. So I just put in the Wesco 440kit. Now its making a funny noise when i give it gas, its like a chirping noise. It is also extremely hard to start. I just put new jets in today. My friends and I can't figure out what is wrong. Please help.

 

sounds like you muffed the timing marks

 

So then what can I do to fix that?

 

Its a Honda, sounding like a can of rocks is perfectly normal.

 

Did line up the timing chain or gears correctly when you put the motor back together? Thats what I am asking sorry, if the mark and I am not sure how the honda works if off meaning the valves are not exact you will loose compression get preign and exhaust and will be way down on power.

 

 

Check the timing.
Double check your valves are in spec.
I bet most of your issue is carb related. The ex can be a pia to cold start even when running mint. 40-42 pilot jet will help with the cold start. With a 440 your main should be in the 160-170 range.
Adjust your F/A screw 2.5 turns out from seated. You can buy a special tool to adjust the F/A screw, buy it....

 

Also check for air leaks.