If the main beams are rotting.....you will need some jacks and new beams to replace the rotting ones.  Dirt foundation? or dirt under the beams?  Lots of moisture?

the foundation is elevated out of the dirt.  What happened is the rain over the years sat on the stoop, and just sat there and rotted it away.  This isn't moisture from the ground, its from the rain that sits on the level stoop.
 

 

 

 
This is a few feet off the ground, so my long term solution is to put a cover over the door in hope to cut down on the rain on the back steps, and seal the heck out of it.  But... I figure that wood will keep rotting until then, so what do I do with the rotten wood?  

You can try to scrape the beam down to the good wood (if any) and then replace what you removed with a piece of pressure treated wood. You are going to need to keep water from the porch from flowing back towards the house. You may need to pry it up a little bit and tilt it slightly downhill away from the house.  Whatever you do, it will be a pain.  Good luck. 

Yes, that is the main set of beams that the house rests upon.  They go all the way around the house along the concrete foundation.  

That sucks! I know your pain. I was up in my attic to run 25' of hdmi cable down a wall. I went to drill the beam out up top and it just crumbled from termites. I shined a light down the inside of the wall and they are on the 2x4s from the ground all the way up in about a meter wide space. 

Based off what I am seeing, the main issue is that the slab you step down onto from the door is either level or angled back to the door. You need to make sure to angle the slab away from the house for drainage purposes.
If that is not possible, you need to waterproof the exposed wood with some sealant, otherwise this will happen again.

So here is a "cross section" of my house.  I can see right into my basement.  i removed all the material here.  There is still some rot on the other side, but these is what I am working with:
 

Violence,  should be able to sister the beams to the stubs off the old ones

 
Agreed. Id go with a biscuit'd 2x6 or is that 2x8? And sister this about 3-6 foot if you can on both sides?
 
How are you redoing that subfloor, or least the edge there?
Look at redoing that red pannel, on the outside there?
What about the door jam? 
And what about doing a vapor barrier type window setup for this setup?
 

those are 2x6, id sister in 3-4 ft. lag bolt them together floor wont move. replace door sill, take up the linoleum and replace that one board on the sub floor because its probably rotten. put in a new door sill, replace the door jam and you should be fine. the water wont travel as far as you may think. i had water damage in my home from a leaky shower. wasnt half as bad as i thought. 

Honestly, as long as you have appropriate sealant at the door sill and you make the slab outside slope away from the house, you will be fine.

nateman_doo
I installed a new sill today.  a 2x8, and some 2x6's.  Im scared to show you guys because someone who knows what they are taking about is going to say I did it all wrong, and after the entire day of work, I am not taking it apart.  
 
I still have a doorframe to reproduce, and a foreverdoor to install.

 
as long as its a solid beam from one end to the other either anchored or supported on both sides you will be fine. also slope away like slinger said and you will be good. 

Brimy
You are very lucky it is just water damage and you could just replace the damage, if this was termites you would be in serious trouble not to mention the cost to fix the damage those suckers do. Be sure to water seal the new beams and door jams.

+1 That's true + termite treatment cost.
 
Pictures or it may have happened.... I have little doubt you did a good job , all of your other projects are top notch, Nateman.