I don't know how to naturally get rid of the problems you are having, but I was wondering if you might be able to try an insect barrier cloth? (well, that wouldn't help with a gopher)

like this one:

http://www.gardensalive.com/super-light-insect-barrier/p/82274/

If it is too late for this season you might want to consider for next time :)

Thanks for the info I am definately going to get something like that for next season. Plus I planned on adding another raised garden bed next spring and I'll be sure to line the bottom and sides with some hardware cloth to stop the gophers. I've never had a gopher problem before but I'm guessing I've never made the conditions favorable for them until now.

I'm hoping that mole/gopher repeller is working but its hard to tell since the plants are still shocked from being eaten and probable wont make it but I haven't seen any new damage so thats a good thing.

~Drew~

Found another gopher hole today, not near the garden but still in the yard. I'm hoping it's his retreating tunnel but I'll keep my eyes open.

Have you had a good reliable soil test done yet? What is the soils pH? What are the levels of the major nutrients, P, K, Ca, Mg?
How much organic matter is in that soil?
What kind of life is on that soil?
How well does that soil drain?
How well does that soil retain moisture?
What does that soil smell like?

No good reliable soil test has been done, I've just been adding organic matter.
In the beginning I didn't see any earthworms but now I see about 1-2 a shovel full and various other bugs like rolly pollies, pincher bugs, and lady bugs.
The soil drains pretty well but holds moisture. I haven't had any watering issues.
The soil smells like soil, not bad just earthy.

A soil test is definately on the list so I can see what I need to add.

A good reliable soil test for soil pH and major nutrient levels is one aid a gardener can use because soil pH can affect nutrient uptake and unbalanced nutrient levels can do the same.
In addition these simple soil tests might be of some use.
1) Soil test for organic matter. From that soil sample put enough of the rest to make a 4 inch level in a clear 1 quart jar, with a tight fitting lid. Fill that jar with water and replace the lid, tightly. Shake the jar vigorously and then let it stand for 24 hours. Your soil will settle out according to soil particle size and weight. For example, a good loam will have about 1-3/4 inch (about 45%) of sand on the bottom. about 1 inch (about 25%) of silt next, about 1 inch (25%) of clay above that, and about 1/4 inch (about 5%) of organic matter on the top.

2) Drainage. Dig a hole 1 foot square and 1 foot deep and fill that with water. After that water drains away refill the hole with more water and time how long it takes that to drain away. Anything less than 2 hours and your soil drainsâ too quickly and needs more organic matter to slow that drainage down. Anything over 6 hours and the soil drains too slowly and needs lots of organic matter to speed it up.

3) Tilth. Take a handful of your slightly damp soil and squeeze it tightly. When the pressure is released the soil should hold together in that clump, but when poked with a finger that clump should fall apart.

4) Smell. What does your soil smell like? A pleasant, rich earthy odor? Putrid, offensive, repugnant odor? The more organic matter in your soil the more active the soil bacteria will be and the nicer your soil will smell.

5) Life. How many earthworms per shovel full were there? 5 or more indicates a pretty healthy soil. Fewer than 5, according to the Natural Resources Conservation Service, indicates a soil that is not healthy.

IMO you should diversify the crops greatly. In the bay area you can be growing a lot more than what you are in the winter season. Nothing controls problems long term like having a large number of highly divers crops near each other.

I'll do that at home test tomorrow but I know I don't have 5 earthworms per shovel except for where I'm trench composting and I don't plan on planting in that area until spring and that's only If I expand, probably not the best idea since I can't keep my little plot healthy yet.
It smells earthy and has no bad odor and the soil does compact but break apart easily.

No new signs of gophers, I read that urine on/in their exit holes will speed up the process of them leaving so I may have to try that...

Hey Drew, I have to put in a good word for clover -- it's a legume, and fixes nitrogen at its roots, so it feeds the soil. It's a good soil cover, a living mulch itself. I till my pathways in the spring and then plant clover, and when it grows into my beds I'm happy -- I never pull it up, but let it grow next to things, cooling the soil, shading out less helpful weeds, and feeding the veggie plants. That's my take on clover -- maybe save you some back breaking work? Also, the flowers attract pollinators. I let it go to seed all over the place. I LOVE clover!