Chinese Elm has brown spots

Nice work on the roots. I would probably have chopped the remaining roots much shorter to encourage more root ramification closer to the trunk but that can be done another time if you mant to do it.
No problem chopping a Chinese elm at repotting time.
Chinese elm can be chopped as low as you like. Elms have the ability to throw new buds from the trunk and from the exposed cambium at the chop site so there's no real need to restrict chops to a side shoot or branch.
If the trunk is still unstable you can tie it to the outside of the pot. I sometimes use twine or wire wrapped around and under the pot then around the trunk. If the lean is only in one direction a simple wire hook from the trunk to the rim of the pot may be enough. Your tie down only needs to be in place long enough for the new roots to grow into the soil - maybe 3-6 months, depending on conditions, etc.
Thank you as always.

I went ahead and chopped it lower and it looks better already.
 
It looks like I was too late to suggest leaving it tall like some of the elms in the Chinese garden at the Huntington. These are old pictures, but I do like these unusual forms.

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Those are interesting! But yes, it's too late for anything like that. I have other plans for this tree.
 
I'm looking for advice on this elm. I chopped it when I repotted in spring because it was too tall and any wind would knock it over.

Basically, I'm not sure if I should just keep letting it grow or chop the stumpy part off so the growth goes into the skinnier trunk. Or should I do something different?

The fatter part of the first fork is what got chopped.

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Foliage makes things fatter. Removing foliage does not help that at all. If you have a garden bed you can plant it in it will grow 10x faster than any pot.
 
I'm not sure if I should just keep letting it grow or chop the stumpy part off so the growth goes into the skinnier trunk. Or should I do something different?
Well...
I have other plans for this tree.
The first question you need to answer is WHAT do you have in mind for the tree. Without us knowing what you would ee as future image, it is impossible to make recommendations. It is already a little bit older -I had to check how long ago you started this thread (!), but not very far developed in terms of trunk thickness. So.. Where do you see this go? A fat trunk, I agree with @jeremy_norbury will develop fastest in the ground, although pots can do it too. But you then need to stop cutting for a bit
 
Foliage makes things fatter. Removing foliage does not help that at all. If you have a garden bed you can plant it in it will grow 10x faster than any pot.
Well...

The first question you need to answer is WHAT do you have in mind for the tree. Without us knowing what you would ee as future image, it is impossible to make recommendations. It is already a little bit older -I had to check how long ago you started this thread (!), but not very far developed in terms of trunk thickness. So.. Where do you see this go? A fat trunk, I agree with @jeremy_norbury will develop fastest in the ground, although pots can do it too. But you then need to stop cutting for a bit

I am avoiding ground-growing because I may be moving in the next year or so. I don't want to plant my trees in-ground only to have to leave them there or dig them up at a bad time of year.

Also, I'm not worried about a super fat trunk. I think there is much beauty in skinnier trunks as well as fat ones. For now, it's in a pot that will allow for plenty of growth for the next couple years.

It sounds like you guys are saying to just let it grow, which I am cool with.

I'm thinking of a simple upright bonsai or broom for this tree, something like this maybe...

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