Cat,
It took me a few years of ownership to get a dry bilge, it's a full time job keeping the water on the outside of the boat it seems!
If you don't have a dripless packing gland that is going to mean that you will generally have water in your bilge although I understand that there is some packing material out there now (gortex?) that allows one to run with virtually no drips of water.
Personally, I think the next biggest sources of water in our vintage of boats are the windows. Much has been written about trying to solve that source of leaking water.
Water will also run around the lid to the aft cockpit locker and drain down the rudder tube and find it's way into the bilge. In the winter I keep a cover over the area where the emergancy tiller attaches to prevent water from entering the cabin there. Also, a few dabs of silicone to direct the water in the rain gutter around this cover onto the cockpit floor instead of into the rudder tube helps considerably.
If you don't have a cover over the companionway rain water can come in at the base of that hatchboards. Some owners have added a small strip of wood here to help prevent this, I have an insulated hatch cover that snaps on.
I agree with Jack that two inches seems a bit excessive, but when your bilge pump shuts off water will run back down the hose and re-enter the bilge so that there will always be some water level that the bilge pump cannot pump out.
Take care, DanM.