The last area i'd like to address is the junk inside the sills itself, where the water drains from the cowl into the wing i suspect there is a buildup, how do i actually access this area?
Pull the plugs, fish out all the leaves you can. I put the vacuum on one of the holes and use various instruments of poking things to push the leaves towards it. From underneath, you will find all the drain holes, use a small screwdriver or a wooden skewer or similar to unblock them. Then use a hose to rinse out smaller debris. Repeat this process until it's all nice and clean inside.
Once you've got it clean, you should be able to set a garden hose up so that it sends water down through the vents in front of the windscreen, and you should see a steady stream of water coming out of all of the drain holes. Hose on the windscreen is generally a very effective tool for finding leaks at the front of the cabin.
If you want to go for 10/10 result, once you have the sills clean and dry you can get some aerosol cavity wax and coat the inside of the sills with it (it comes with a long bendy spray tube for access).
With the blower motor, again it is designed to permit some ingress of water, and it has a drain to let the water out under the car. If it is leaking there is a good chance that its drain is blocked.
Avoid using silicone IMO, these parts keep your cabin dry because they have drains, not because they are sealed up.
