I don't know much about this subject, but I imagine that I could compare the BIOS contents against official firmware to check whether it has been tampered. Is there any tool that can help me with that? As for cleaning methods, in the case of suspected BIOS infection by malware, as noted in a similar question, one way to clean the BIOS is to use a hardware jumper, but most of the time I think a firmware upgrade could do the job.
Probably the only program that would compare your BIOS firmware to the official firmware is the original firmware loader for the firmware already loaded. It is the only thing that probably has the original checksum.
Removing the jumper may clear out your settings, but the basic firmware and the bad code will probably remain.
The best way to ensure your firmware is not infected is to flash it again.