I've been going through the same issue for the last season and a half and have identified three things to help.
1. Boat tightening. Like you said, tighten all the screws, fill in anywhere the plastic is thin, check the glue around the drainplug, etc.
2. Drytop. If your drytop doesn't have good waterproofing, it will get wet and water will drip in through the fabric. This lets in a surprisingly large amount of water. Tight gaskets, etc. help too.
3. Skirt. A good skirt makes a huge difference and it sounds like this is probably your problem. Tight to the body and tight to the cockpit, obviously are important. Mine lost it's waterproofing, wore thin, and got holes eventually. When I got a new skirt, I was bone dry. I have had 100% best experiences with my Snapdragon and will never by a different skirt as long as they keep it up.
"The world would be a better place if everyone kayaked."-Brad Ludden (Valhalla)
"You only get one chance to run a drop blind."-DD