Sounds like there is inappropriate flashing in between the deck and the home... common and no excuse for it. But, that is besides the point here.
Did your inspector mention what he thought the cause was. My guess it is that when it rains, the water rolls off the roof since there are no gutters, and then runs back to the house. If there was metal flashing between the deck and the house, no big deal. If not, then the water finds it's way into the framing and rots the door framing. Whatever the cause is, you need to find out before you ask for repairs. Otherwise, the sellers could "repair" it in an unacceptable way. The inspector should have noted if he saw any flashing.
The roof need replaced.
These are not walk away items IMO. At least not yet. Ask the sellers to put on a new roof, specifying the type and grade of shingle. Same with the water intrusion at door.
The roof needs replaced

Ask for a roof inspection....and go from there. The roof is THE most important protection of the home, old or new. I learned recently that one leak in the roof is indicative of lots of roof issues.

Not true at all Sasafras. A leak in the roof means there is a leak in the roof. Get it checked out by a professional roofer, and go from there.
I have seen many homes with a roof leak where it was a simple fix.

We are getting a few quotes on the roofing. I realize I left out the mold issues - there is mold across the kitchen ceiling (where the roof was leaking). The foundation beam below the french doors (I don't know what it's called) has rotted, from what the home inspector could tell. There is mold in the crawl space. I think that was all the mold.

The inspector thought the door rot was caused by the house not having a cement foundation under that portion of the house (it's about the last 25% of the dining room - 3 ft or so). It was hard to tell, but from inside the crawl space he said there was a cement wall suddenly - before the house ended. So he thought the moisture was coming up from the dirt.

I was hoping to have the full report last night, but I should definitely have it today.

The seller had previously indicated that she would not be coming down any further in price or offering repair credits, since these items were in the disclosure. The house is currently priced at about $135 / sq ft in an area where homes are typically $170 / sq ft. It's not clear if she knew the extent of the damage though from the disclosure. She has since moved out of the country, so my hope is she will still be willing to negotiate for the sake of selling the house.

Yep, the sill plate and/or the rim joist usually get the water first, so if you see stains and rot on the interior of the door jambs, then there is a good chance that some of the rim joist and sill plate need replaced. The mold is a secondary problem... get rid of the moisture and you will get rid of the mold problem. You should still probably have a quote for the removal of the current mold though.
I would get all quotes in order, and demand that the seller pay for all or some or you walk. See what the seller says. Never mind what she has already told you. that has nothing to do with it, since no one knew the extent of the damage. If she says no to a price reduction and no to the repairs, at least you know what it will cost to get it repaired yourself if you decide it is worth it. Not too much else you can do. Good luck and keep us posted.

I would walk! but you really want it so deal with $$$

Thanks for the input. I spoke to my realtor today. We are going to get quotes for all the work and ask the seller to contribute half the cost of repairs if it's less than $40k. If it's more, then we'll walk. My realtor said he expects the quote to come in at $30k for everything.

You mentioned that some cement work under the house stopped then the part of the house continuted. My concern is that part of the house either was added on or changed probably without permits. You need to check with your city/county to see if permits were pulled and/or done illegaly. This could be a big problem in the future when & if you sell.

Marie - thank you for the information on how to check that out! I found the property report online, and it looks like that section is part of the original house. After speaking to my husband , our realtor and the property inspector, they said that 3ft section probably has a concrete slab underneath. Apparently the crawl space was too small for the inspector to get all the way back there. I stopped listening after he said "there might not be a foundation in that section".

Our realtor has a contractor going over to quote us on all the work, and have him inspect that area further. We will not buy the house if there is no support there.

From the property report I pulled, I was able to see when the addition on the other side of the house was put on, so that confirms our suspicions about the age of the roof and some other components in the house.

Thank you again, I wouldn't have known to do that.

My co-worker recommended these forums, and everyone here has been a big help.