Your house has been dumping water into the foundation for 12 years, and you just put gutters on. Tell me that the gutters go to downspouts and if the downspouts don't connect to a storm drain, at the very least they are terminated onto splash blocks that direct water AWAY from the house.
Next, call your homeowner's insurance agent. Tell him you suspect you have some structural problems due to improper construction techniques (no gutters). The agent should send an inspector out to examine not just your rotten joists (and posts I suspect) but also your footings and foundations for undermined soil conditions.
You describe a VERY SERIOUS problem. You need to adress this ASAP. With any luck, your insurance will help with the cost.
You will need a professional inspection by a licensed structual engineer, to determine exactly the extent of the damage. You will then need a professional contractor to work on replacing the structural members under the house. If the foundation needs replacement or repair, the house may have to be lifted for that.
I don't want to scare you unecessarily, but I don't want you to ignore this either. Do it today!