Is it safe to assume you've narrowed the leak to being above the waterline?
We bought an '87 last fall. In the process, we looked at 6 different Cal 28-2's and there are a couple of spots that consistently showed water penetration (looked at model years 86, 87 and 89).
The first is the quarter berth area, all the boats we saw were effected here to some degree. Usually the owners had a piece of plastic or a bucket in the area directly behind the engine. Water stains were obvious on the wooden cover over the seacock/shaft seal. It turns out that in ours, it's from one of the pedestal guard feet. In heavy rains, we'd get a small pool of water below the cockpit. I removed the wooden headliner above the engine seacock cover to expose the helm cables and pedestal cavity. With a hose in the cockpit, we sprayed different areas. Water slowly began to drip in when it was aimed at one of the pedestal feet. I covered that foot with silicon (for troubleshooting only - not a permanent fix), and the leak went away. It's on the list to fix correctly this off season (remove/core/epoxy/rebed).
The other area is the aft stern quarters above the teak shelving (port side). Ours no longer leaks here, but the fabric hull liner shows that it did in the past. This was seen on each of the other boats we looked at to varying degrees. I don't know if this is due to the teak toe rail bedding or not as I couldn't get water to penetrate this year with a hose.
About half the Cal 28-2's we looked at had 'checking' on the aft stbd toe rail - ours included. However, this area does not leak on our boat. Others showed evidence of the chain plates leaking and 2 had issues with their opening ports. I didn't see any evidence that the fixed port lights leaked on the boats we inspected.
It's all just anecdotal, but maybe these are some areas you can check out.