I used to do floor leveling and foundation repair. If 40% of the floors are rotted. Run, unless you are willing to invest a lot of $$$ into the repairs. It's not as simple as just tossing in some new joists.
First thing you need to do if your serious is get the basement / crawlspace dry. The best and easiest way to do this is to improve ventilation and make sure the terrain isn't part of the reason water is getting under the house. If it is, you are going to have to potentially move some dirt around and or add drains. If it's not a problem then move on to modifying the foundation. Main thing here is airflow, you want good airflow under the house to keep it dry. Easiest way to do that is add vents into key locations, and not at the ground level obviously. Once that's done and it's dry, you will need a hazmat suite and go in with some serious chemicals to kill the mold that i'm positive is present and very hazardous. Once all the mold is killed, you need to rent or buy one of
these and take measurements from the side of the foundation and several points to find out where the jousts are sagging, which they will be if the damage is as bad as you say. Depending on what you find depends on how you proceed with the repair.
What we commonly did in this situation if the damaged floor joists weren't complete garbage was sister in fresh joists next to the damaged ones after leveling them out. We accomplished the leveling by nailing two 2x10's together making a beam we used to lift the joists to where they SHOULD be. Then sistering in the new lumber. Make sure the new joists are sitting on the foundation. Also check the *sigh* can't recall the term, but the boards between the foundation and joists and the outer ones to make sure they are not rotted. If they are when you go to level the floor, lift it higher to take the weight of the house off of those pieces and replace them, then sit it back down and proceed with the joist repair. In some cases you may have to install the joists prior to this if the existing pieces are so rotted they can't take the load, you will know pretty quickly as when you start to lift them, they will start to be crushed by the beam you are using to lift.
As for the jacks you use. PM me and I can tell you how to build some if you can weld. DO NOT USE HYDROLIC JACKS BY THEM SELF. And make sure all your jacks reguardless of type are level and wont kick out. If one does and you are close to it, you are asking for some serious hurt, injury or death.