I let the bike sit in the rain for 2 days and tried to start it and the bike ran really rough for a few seconds then died and wont fire off ever since . is this the spark plugs due to rain ?

 

Spark plugs are sealed and there really wouldnt be a way for water to get in there.

Water could be in any number of plugs possibly, let it dry out first

its odd because in reality these are meant to operate in wet conditions so this really shouldnt have happened like that

 

Here's a link to the service manual if you really want to remove the air box:

2008 CBR 1000RR Service Manual with Search Enabled