All these things your so worred about should have been addressed with the home inspector before buying the house.
You say you had or are having windows installed. Any of that rotted T-111 needs to be addressed before windows go in.
The reason it rotted and will rot agin even if it gets replaced is because it's sitting to low to the ground. It should never be closer then 12" from the ground or splach back is going to distroy it.
If it was my house I'd cut it out 2' from the bottom, install OSB board the same thickness over that area and vinyl side over the whole wall. That way there's almost no maintance.
When you remove the T-11 you may just find that mold you were looking for plus rotted bottom plate and damaged insulation needing replacing.