Sill plate leaks and leaks in general

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Just for background, I work in the warranty department of a builder in Colorado.

Sill plates: Any brick or masonry facade will have moisture penetration. The mortar is porous and will allow water to get behind the brick. Hopefully, the masons put a water barrier behind the masonry such as tar paper. Now for the problem.
1) The transition from the waterproofing behind the stucco to the foundation is allowing water penetration. Likely the lower courses of masonry need to be removed and some sort of ice and water shield needs to be placed in a manner to shed water off of the sill plate. Copious amounts of silicone caulking is never a bad backup. Please note all this is done from the outside. If you do it from the inside, even were you to completely seal the leak from penetrating, you would still have wood members that are getting soaked and will rot and/or grow things.
2) In order for this to be a problem, it is likely that there is excessive water getting to the masonry. There should be a drip edge where the normal siding/stucco/whatever transitions to the masonry. If there is no drip edge (a piece of flashing that directs water away from the masonry), then that too is a problem that needs to be fixed. The drip edge needs to be installed behind the water proofing of the normal material (if you have this problem, it is likely a stucco house). This will require significant repairs to the stucco.

Water intrusion in general: Assuming that the wood is not rotted, there is no reason that you need to replace boards just because they got wet for a couple of days. They probably got wet during the building of the home anyway. The crucial thing is to make sure that you allow the wood to dry out. Often times, this can mean exposing the wet area and letting it dry for a week. Though this can be very unsightly, it is essential that you let the wood dry before covering it back up.

Hope that helps.
Scott