You can manually run cron scripts by using:
sudo periodic daily
sudo periodic weekly
sudo periodic monthly
For repairing permissions, you need the chmod and possibly the chown command.
chmod 750 filename
(Gives the owner of the file all access, the group Read & Execute, and everybody else no access)
chmod is a complex command. It can be used in a numeric mode, like this:
chmod 740 file
The first digit '7' represents the OWNER of the file.
The second digit '4' represents the file's GROUP.
And the third digit represents ALL OTHER USERS.
Basically, you use 4 for read access, 2 for write access, and 1 for execute access, and simply add them together. So to give others read and execute access to a file, you'd add 4 and 1 to get 5, so the last digit is 5.
The other way of using chmod is using letters like these:
chmod a+x file
u - User (owner)
g - group
o - Other
a - All
... then, a plus or minus to allow or disallow the privilege, then ...
r - Read
w - Write
x - eXecute
So, for example:
chmod g+w file (Give the group write access to the file)
chmod o-rwx file (Take all privs away from other users who aren't the owner or group)
You'll have to do some more reading, depending on what you want to achieve.