It looks like there is some rotten tissue (yellow-brown color) behind your cut, perhaps all the way through the stem... I'm not sure you cut enough out of the plant. Judging from the wrinkles in the stem, it looks like the affected (rotten) part extends well around the part you cut out, even if it is not soft (yet) to the touch.
You can leave it as is, and see how it recovers. The danger of cutting even more deeply is you might not have anything left afterwards.
And yes, the bottom part does not look good. The rot there may actually connect with the part above through the inside of the plant. It's hard to know. This whole situation will probably resolve itself one way or another by spring.
Do not water again for a month or more.