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Found a struggling Japanese maple at a local nursery, had to chop the top 4-5 feet off as it was dying. It is mid to late fall here and wondering if I s hould do some more pruning on unhealthy parts of the tree now before winter? I’d like to get it in a training pot come spring as well.

Pruning dead parts is ok anytime of the year.

However, in my experience and climate it is next to impossible to identify this time of the yesr if a branch is dead or just dormant. I was totally sure one of my garden tree maples was dead last authum. Even bought a replacement tree in authum sale. But it flushed leafs as usual in spring except for just a few dead twigs.

I think that you may have cut a lot of healthy parts already and would not recomend pruning anything more.

Not until late spring it is possible to judge health of the tree. I always advocate that we only repot healthy trees. Since repotting season is before leaf break and you have already cut a lot of possibly healthy parts, I would not do repot come spring, but wait another year.

Thank you. The only portion cut had died before the spring, I had been watching this tree at the nursery hoping to get a good deal on it. Will leave the remaining until next year.

Some japanese maples should be treated with care when cutting, they are very subsceptible for molds and diseases.
- use only clean or better disinfected tools
- close the cuts with treewax or similar
Probably you can read the best time to prune ist march-april but at that time the maple is blooding a lot, if you prune it 6-8 weeks after the tree sprouts, you will have less problems and the cut will heals better and faster.
Fall ist not the best time but now its done and for deadwood OK , if you dont used clean tools , cut it again and seal the surface.