I have some spam messages in the log which which did not get corrected when SS classified them as good. They are old enought that the message data has been purged from the SS Log and the Trash folder in Apple Mail has been emptied. The option to mark them as spam in the Log is grayed out. Is there any way to correct these mistakes at this point?
You could try searching for those messages in the Good Messages tab of the Corpus window.
Is it preferred to mark it as spam from the Rules window if it allows it? Or is it just as good to find it in the Corvus?
Training from the corpus or log is best. The rules windows do not show messages or allow training, though you can disable or delete unwanted rules as a last resort if you can’t find the messages to train.
Trying to do too many things at once 
I actually meant was it better to train from the Log or the Corpus? (don’t know why I said Rules)
There is no difference except that the log prunes old message data.