It can get quite tight here but boats seemed to come and go, we only stayed for one night. You need to apply for a permit and take your boat to the customs/police dock to be inspected. The basically confirm you are a non San Diego resident and ask questions about the heads, your life jackets. Then they will issue you a permit for 30 days.
We used the dinghy dock to the far side of the CoastGuard Station. It was very full and everyone had their outboards, fuel tanks and dinghy’s locked on. We walked to the airport from here to clear out, as a foreign flagged vessel you need to get your 1300 form stamped by CBP. As of writing it is situated in terminal 2 , go to the sign that says Zone V on the side of the road and it’s directly inside the building on the ground floor, opens 9-5 Monday to Friday. If you wish to clear out at the weekend then you’d need to go on the Friday. Telephone number for assistance is : (619) 491-2601 ( NB : this is not the office number but they will assist you. )