As for quests, there is extremely few of them. You listed all of them already or almost all. The rest is derived from the core quests you described.
- Acquite ability (Find NPC + Talk to NPC + Find item as a payment)
- Create item (Acquire ability + Find resource)
- Interact with object: "Read ancient runes from the astral pyramid and press the right one" (Kill Monsters to get to there + Acquire ability of linguistinc + Pass INT check)
Then you create chains (talk with NPC about liche slaying, find the old sceptre, learn ability of repair, find crystal of power, create new sceptre of power using repair ability and crystal of power, kill monsters to reach tomb of horrors, use sceptre of power to kill the liche, open the door using thievery skills and free the princess, talk with princess and pass CHR test to make her into marrying you).
As for stats, skills, abilities (these are the same thing from designer's perspective, just arrange this way for player's convenience) it all depends on your mechanic and storyline. Combat system determine mostly the stats, skills are more flexible and you can use some for storyline purposes (access area: taming to tame a pegasus to make it fly you over mountains, battering to make you money to board the ship to new continent, librarian skill to make you find the forgotten teleportation spell which will get you to the new location, etc).
I would start with combat mechanic. This is the simpliest way of finding your stats.
