Since you haven't got any responses yet I'll give what (little) I know about what you're asking to give this a bump. The first place I can think of since it's essentially in the east county is Mission Trails, plenty of fire roads and mixed use trails. Los Penasquitos is one that runs from Poway or there abouts, all the way to Torrey Pines. It is mostly mixed use though.

As far as shops that organize cross practice, I don't know offhand but suggest Anywhere Bike Repair in Kearney Mesa, ask Stu I understand he's into MTBing and knows plenty of places in the east county where he lives.