Hmm, sounds like a major repair job.
Before starting you may want to check the mast step. A lot of rain water comes in to the boat along the mast. The mast step screws could leak water in to the tank.
Some older MK2’s did not have sufficient support for the mast and the GRP below the step could have cracked. The worst case I have seen was a mast that sank about 10 mm in to the supporting GRP. I am not saying your boat is one of that series but it would not hurt to check for cracks under the mast step. If however, you do have one of these boats you are in for a nasty repair. You need to laminate a piece of wood under the mast inside the tank, through the inspection hatch. It sounds impossible but It has been done. See here: http://translate.googleusercontent.com/translate_c?hl=en&ie=UTF-8&sl=da&tl=en&u=http://www.wayfarer.dk/index.php%3Foption%3Dcom_content%26task%3Dview%26id%3D86%26Itemid%3D33&prev=_t&rurl=translate.google.com&usg=ALkJrhiQF4IEcwGVgYi6c-5AZVRLUR2U2g
and here: http://translate.googleusercontent.com/translate_c?hl=en&ie=UTF-8&sl=da&tl=en&u=http://www.wayfarer.dk/index.php%3Foption%3Dcom_content%26task%3Dview%26id%3D87%26Itemid%3D33&prev=_t&rurl=translate.google.com&usg=ALkJrhjfyzTPzzF8-tX7RG5erPYXs0VcQA
What I am trying to get across is first look for the simple problems and simple solutions and only if they fail go for the major repairs. Find the leak with some soap and then decide if it needs major repairs or only a quick fix with some sealant.
If your boat has been stored ashore your leaks could still be higher up. Water has a nasty way of finding its way in to the tank. Rain comes from above and under a cover it could also be condensate leaking in to a the tank. Maybe a few drops at a time but after 6 months that could have accumulated in to several liters. Or maybe it is just a case of a poorly closed bung?
P.S. Blame Google for the poor translations.
And to please CP: Never use anything on a boat that starts with the word “silicone”.