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The fire wall wiring should have a grommet like the one your speedometer cable has, or a electrical box. Either way it should be sealed. The hood cowl is supposed to let water in but it has a drain on one or both sides of the cab, they are possibly plugged with debris. Remove the cowl and try and clean it out. There should also be a plastic screen under your cowl that covers up the oval holes to stop debris from getting farther down. I am uncertain on the kick panel leak from the photo. Could be it’s ok to plug it or there is supposed to be a bolt in there to hold the plastic kick panel on. I’d start by replacing the grommets on the fire wall and possibly running new wires. I don’t like how that on has a wire splice in the grommet, it’s too big and will allow it to leak. Good luck on your build.
Yes there should be a weatherstripping molding between your hood and cowl. I wouldn’t adjust your hood unless the front is sticking out farther then the end of the fenders. You can buy a new molding at for bout $13 bucks.