I'm an engineer and sistering the joists is the right answer. I also remodeled a 100 year old house from stem to stern, and that is where I really learned about this stuff.

One thing to note is the ship-lap was the sheeting.

I'm not sure about your jacking technique though. When you pick up the wall, with the floor go with it, or will the wall just pull away from the floor? Is the existing floor deck sagging over the rotted area or is it flat still?

I know the crawl space is a bitch on these old houses (trust me I really know), but couldn't you just angle the sister joist in there then smack it into place with a heavy hammer? You could use your bottle jacks to spot jack the flooring on either side of the joist to provide relief to get the joist in there. Just put a 4' chunk of 4x4 on the end of the jack and give yourself that 1/4" of space you need to get the joist sistered up. Hopefully by the time you get all 10 joists done, you will have raised the plate at the exterior wall enough to get the rim in.

If you do try and jack from the outside, do it slowly. Even then there is a really good chance you will f-up the interior finishes. I figure to jack the exterior wall enough to get clearance at the next girder line you will have to move the wall up quite a bit.

It will be more dirty-sh!tty work, but I think the single joist method would be what I would try.