I used to ride the path around the park quite a bit, and used to get many flat tires. I don't know if it was my imagination but it seemed I almost always picked up the thorns on Balboa between the river and Victory. I always ride the street there now and haven't had problems.
As far as night riding I'd recommend Chandler or Riverside for east-west. I've never found a very satisfactory north-south street, Whitsett's not bad and neither is Colfax. My general rule of thumb is to use major streets that don't have freeway on/off ramps.
Of course get some good lights. I've used the big Cateye taillight during daylight and have been told it's visible a couple of blocks away and I've complimented on it's nighttime visibility by motorists a few times. The Planetbike Superflash also gets great reviews. Of course you'll also need a front light to be legal at night.