2003 Yamaha R1 trouble codes

[rkingw]

I replaced the battery which tested weak after 7 month winter storage. Now I have the engine trouble light on and a trouble code, 11 & 21 flashing. Engine cranks over but no firing. Bike ran fine last fall. I removed the battery other years after storage for recharging but never had this problem. I also replaced the spark plugs before the new battery was installed. Any input would be great.