My plans are:
Risers: 1/8" plywood, cut to size, nailed to existing riser, putty holes, paint cream to match the trim all over the house.
Treads: oak treads, cut to size, dark stain + poly, nailed or screwed into place. Possibly some cove molding under the lip of the tread, since it'll be overhanging about 2".

My questions:
1. I'm planning to cut the treads to size and stain/poly them before putting them into place. Do I use nails or screws? I used finish nails on the trim around the top and it doesn't feel as secure as screws would. However, if I use screws, then I'll need to plug the holes and then stain/poly just the plugs. And that won't look very even, will it? Do I just have to stain them in place and clean up the surrounding paint afterwards?
2. Right now the pine treads and risers extend past the edge of the open wall. I'm going to cut those flush with the wall. The treads will over hang the wall, but the risers will be flush. But then after installing the new risers and treads, you'll be able to see the edge of the pine boards. I know there's trim you can install (or skirting) but then you'll see the edge of the trim on the riser. What's the right way to do this so you don't see any raw edges?

Unfortunately, anything you do to this stair will not cure the code issue...the rise and run will remain the same.

My concern over the raw edge is more about the riser than the tread. Any thoughts there?

I know I can't properly "fix" the 9" (at least without replacing the stringers), but at least the treads will be 11" deep so that one's whole foot can fit on it.

I'll definitely do mitered returns on the open treads.

when I built my house years ago, I did just what casey recommended. Treads are stained, risers and stringers are all paint grade poplar. I cut the stringers just as he described. The vertical cuts were mitered to join up with the mitered risers, the horizontals are flush cut and butt to the underside of the tread.

A few other details but those are the basics.

I was tool-poor back then, I remember doing all the stringer and tread cuts on the table saw. Ah, some things you'd rather forget. Or keep to yourself! lol

I cut off the end-grain ends of the oak treads and added mitered returns. Also done on the table saw.

But the joinery is still rock-solid, the miters tight, and the stairs still look terrific.

Thanks for the input. I may be back.

Next moved on to my big miter saw, got it figured again on the scrap wood, but found, halfway through the maple, that it's not quite big enough to cut to the edge of a 1x10. Finished it off with a jigsaw.

Jigsaw does have both-way miter. That's the plan on the next try.

I'm thinking I'll just keep the lower edge square instead of routering it into something more decorative, and run it all the way to the floor. Then I'll cut the baseboard at an angle when it runs into it, and butt them together.