The in transit figure ought to be adjusted for industry closures: indeed, this ought to be present in Standard, which also has an in-transit number. However, in Standard, industries do not close automatically: they can only be closed by being demolished by the public player, so this may have been missed. Can anyone confirm whether this issue still exists in Standard or whether it has been fixed in a more recent version? If it is still present, then I shall move this to the Standard bug reports board.
The sheep farm all closing without being upgraded is likely to be in large part a matter of chance, as whether an industry upgrades or closes is in large part random.