I'm certainly no expert when it comes to the electronics of a Gen II, but it'd be my guess that you got something put back together incorrectly when you installed that new battery. Double check all the wiring you had to displace in order to get at the battery box....and pay very close attention to the big clusters of connectors that plug directly into the ECU. If someone has severed any wiring into either of those connectors to add in a speedo correction device, or a PCV module, be certain you didn't pull any of their connectors loose from where they splice into the existing ECU wiring.
*************edit************************
According to the service manual, fault code 41 is only the lean angle sensor code. So, most likely you have somehow mal-adjusted your lean angle sensor when you went after exchanging the battery. If memory serves, it is at the lower, front side of the battery box, and would have wiring attached. Refer to pages 8-57, 58 in the service manual to see how to test it.