Some things that have not been said yet about the hood and hood gap and closing the hood.
The proper placement for your hands to close the hood is NOT at the front of the hood by the nose. It is about 6" inside each hood louver, toward the forward edge. Look at where the hinges attach on the other side. That is where you want you hands. I do go slightly forward of that to the forward edge of the louver (but 6" inward), but think about this... The resistance to the hood closing is the springs on the hinges. So push on the hinge, not a plastic lever 2 ft out. I mean, the front of the hood
Anyway, I stop right at the point the latches are about to catch, and then give it a firm push.
Spraying the latches with a little WD40 will help immensely with them snapping closed. Do not however lube the hood hinges themselves. Just the latches by the nose.
Things to look at in regards to where the hood stops when it closes at the front are yes, the bumpers, but just as importantly, the latches. The latches can be shimmed up and down, and major changes in the bumpers should be accompanied by an adjustment to the latches. Otherwise you're going to stress the latch area of the hood.
The hinges and latches both mount to the steel frame of the car. The nose, or fascia, or bumper cover, mounts to a large piece of glass reinforced plastic the entire width of the car, known as the core support. That big piece is shimmed to the top of the lower front frame horns. Moving it up and down moves the bulk of the nose up and down, like at the wheel openings. Like where the hood gap is most noticed. That is not a 5 minute job to adjust the core support to the frame.
The edge of the nose where it meets the hood, in between the headlights, can be adjusted up and down a bit by shimming it to the bumper reinforcement bar aka rebar. The rebar is a big piece of green structural fiberglass that after the nose gets scuffed in an impact, it gets crushed next. With the hood open, you can see the factory black push in pins that attach the bumper cover to the rebar. You may or may not be able to see any shimming.
The headlights can also be shimmed to fit the opening better, but please note that the gap above the headlight is by design, to allow air in that exits the louvers above the wheel wells. Closing that gap as I know some have done, will affect your aero balance and possibly engine temps by a bit. It is best to leave that gap alone unless you are a poser and never drive fast.
Your water leakage issue could be coming from the seals at the heater core area above the passenger footwell. With the hood open, right in front of the windshield is the heat and AC. On top of it should be a couple small hoses that go into the car. Look for cracked rubber there. If so, you should be able to fix that with some silicone. Just be careful not to smear it all over.
Back to the way the car is built, you can see in this pic the bracket at top front frame rail. On top is where the hinges and latches mount. On the front face of that bracket is where the rebar goes.
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In this broader view, the lower front frame rails is what the core support sits on. That is where it is shimmed, and that is where you should adjust the nose to the hood. Adjusting the hood to the nose is different just to clarify.
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Here is the core support sitting in front of the car uninstalled.
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Here it is on the car. Notice the wheel well area. You have to move that big hunk of black plastic up or down to make the nose fit the hood, as there is not any adjustment between the bumper cover and the core support in that area. Once again, the procedure to fit the hood to the bumper is different.
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