You mentioned "the thru-hulls under the boat are not the problem". By that do you mean, for example, a transducer or livewell pickup is not the problem? I take it you've visually verified that water is coming in, but not from those areas? Have you ACTUALLY seen water coming in somewhere, or is this an assumption based on where it is pooling? If you can see it coming in, that makes your job a heck of a lot easier.
As mentioned above, that siliconed hole is no-no. If that's the culrpit, not only has water been seeping into the boat, but depending on how that hole was dressed, there's a good chance water has seeping down into your transom wood core, filling it up and rotting it. All depends on how long it's been going on for. Some exploratory holes would be in order near the bottom of the inner transom glass (no reason to drill more holes on the outside) and also at a couple points below the hole. Drill until you get to the outer transom glass.
When you fix that hole, don't use 5200 if the hole will see the sun or, really, even reflective rays. A better solution would be the MarineTex/PC-11, or even better, thickened epoxy and glass. But, as mentioned, you'll definitely have to first make the hole bigger to get rid of any traces of silicone and (possible) compromised wood.
If you still don't know where the water is coming in, you can try taping paper towels in key areas - even if they dry out, you can still tell that they were wet. Another way to tell if it's any of the hull bottom thru-hulls is to fill the bilge with water - sometimes water will trickle back out. Although sometimes it won't as it will only trickle IN due to the pressure.