1. If you did not accept Corinna's quest to teach you Aura of Command, then there is no reason why Penumbra should wait for you. Since Corinna is dead - that's it (this also is the reason why the basement is not accessible, as this would be the place of teaching)
On the other hand - have you been in Lepthin's basement and tried the "special treatment"?
2. There is an old man, who approaches you for some money - if you give him a minimal amount, he'll tell you about the gems, which triggers the quest
3. Finding SHRIMPO? in the northeastern corner of the graveyard are some graves - if the names on them are read in the correct sequence (S-H-R-I-M-P-O), the friend will appear.
None of these quests have any influence on becoming the divine!
