Where does the water in the bilge(S) come from ?

I see water from the stuffing box.  It leaks at about 6 drops per minute with the shaft turning. Very little during non operation days, but does leave a little water around our little Yanmar YSB 8.   How do others remove this water  ?  I've been using a small hand pump and a sponge.

Do you get water in the Lazarette, down by the fuel tank and batteries ?

I get water under the front cabin step, and have a small bilge pump there, but little water at the dock, some after being underway.  Can water from the keel bolt hold end up there?  So far not much seen.

Are there, Limber holes," between the segments of the bilge that allow water to run move fore and aft ?

Impressed that this boat leaks litte during heavy rains.  Been dry after several days of heavy rain.

Steve,
I found a few areas of where I had a water issue. Shaft log info I'll also note.
Biggest one by far was a very small leak in the cockpit drains that run into the keel trunk.
It's very important to use smooth wall tubing for this. Keeping a downward slope from start to finish helps too (winter storage in new england makes it critical).

A less likely area but was a problem for me was due to a prior owner running screws holding the stairs into the front cabin. They were so long they passed through the keel trunk. I stumbled on it one day when doing some keel inspection with a flash light.

I windows and handrail stanchions I've found have leaked. Rebedded them with a 3M material and avoided the poly sulphone (don't use it anymore).

Shaft log:
After launching with the new motor I tried the old fashioned teflon flax packing. Worked but still dripped more than I'd like.
Tried the new gore stuff after reading some posts on the web. It really does work. I coated it with water proof grease installed it and no noticable leaks. Ran as cool as the flax stuff too.
I also bought the expensive putty stuff but did not install it due to the gore packing working so well. No Drips!!

I found water in the bildge due to the bow eye for trailering.  I loosened it, filled it with silcone and the problem went away.

The keel bolt does not pass through the hull, so no chance water comes from that. The bolt is contained within the hanger box inside the trunk. A unique feature of these boats.

There should be limber holes in each bulk head. Sometimes they get clogged with debris.

When I bought my boat, it was leaking both from the cockpit drain hoses and from around the base of the steering pedestal. Removing and rebedding the pedestal, and replacing the drain hoses and clamps solved that problem.