Superclone Disk Examiner is  a disk utility that will let you verify the checksum of tracks 1-40 and can accomodate certain tracks that might have extra sectors. 

Some additional information about checksums I found at the excellent pagetable.com website:

The on-disk format of 1541 disks uses 8-bit checksums to protect the integrity of headers and data sections. It is calculcated as an XOR of all data bytes. An 8 bit checksum is not very strong: The probability of an undetected read error is 1:256. In practice, it is good enough that it should be trusted for most cases.