Kay, it is important to remember that trees 'breathe' through their roots. When planted, the root flare (where trunk widens at base - if unsure, look at trees growing wild in nature, the trunk widens at ground level, and often on trees with some degree of maturity, you can see where the trunk starts to divide into large, structural roots) should be visible at ground level. If this is not visible i.e. the trunk comes straight down to the ground with no widening, it is planted too deeply. The tree will start to die from the top down. In effect, it is suffocating in the root zone. Also, when you mulch, do not pile it up around the base of the trunk, as this can lead to rot. It should be kept back about 6inches from the trunk. If it is against the trunk, it can look somewhat like a volcano, hence the term 'mulch volcano'. It may help to visualize the proper placement more like a doughnut, with a hole in the middle. That being said, it is possible that what you're seeing is some damage from some rot starting due to moisture being trapped against the trunk. Check your planting level. If you need to remove some soil so that the trunk flare is visible, do so, but be sure that you don't leave the tree sitting in a hole, either. If much soil needs to be removed from the base, you may need to lift the tree up somewhat by placing more soil underneath. If damage isn't too severe, and moisture is no longer trapped against the trunk, your tree should be able to heal itself. Don't be too hard on yourself for piling stuff up against the trunk last year, we all make mistakes, the important thing is to learn from our mistakes, ask questions, and get help if we need it. Good luck with your tree.

Thank you so much! I have pulled dirt away from the trunk but will pull it away further. Now I recognize the root flare you are talking about and this Shishi doesn't have that so it probably was planted a little too deep in the first place :( . Could that be why the new branches at the top have trouble filling in with leaves?
It's been in four years and has grown a little, is usually nicely green in the summer (except for the few longer partially bare branches), each fall it's decreased in fall color until this year which is why I think it liked the compost. We add a little sulphur every spring because the soil is alkaline.
The lesions at the base look soft so I think a slightly rotting look; is that an entry for bugs now and can I wrap it or something to protect it?
How do we go about lifting the tree up and how do I know if that's needed? Since jms don't like their roots disturbed, I'm guessing that's an extreme measure anyway?
The dirt does have a lot of clay so we amended in the beginning by tilling in peat moss and now I'm into 'no till' and putting compost on top. With these temp variations do I need to mulch deeply around my jms and are they safe as long as it's away from the trunk?
So many questions! But if you can answer those I think I can go from there and apply it to the mistakes I made on the other two jms I haven't mentioned (those mistakes are worse but the varieties are easier replaced anyway, lol).
Thanks again, I've already learned a lot from you in your various entries!

Glad to have been able to offer a little help, Kay. I've planted trees too deep to begin with too, and then learned, luckily, before much damage was evident. Gardening is a learning process, the steepness of the learning curve is variable! The depth of planting is very likely the reason for the bare look at the top. Try to pull enough soil away from the trunk so that the root flare or collar is visible. If doing so leaves your Shishi in a depression, or worse yet, a hole, first and foremost, dig a trench so that excess moisture can drain away rather than sit. Then in late winter, while the tree is still completely dormant, but the ground no longer frozen, you can try digging around your tree (you could do this now, going around the tree a set distance from the trunk to get as much of the roots as possible, sinking the shovel in to the depth of the shovel blade). After going all the way around the tree (I'm talking late winter again), try loosening it, taking your time wiggling it and gradually lifting the root ball. When able, tip your tree to the side enough to shove some more dirt under the root ball. Proceed to the other side of the tree and do the same. When you think you've got it, stand the tree upright and check. If more is needed, just tip the tree again and continue building it up. When at the proper level, be absolutely certain to fill in any air pockets under the tree and firm in place. Re-mulch using the previously mentioned 'donut' method. If done in this manner, it IMHO less stressful to the tree than lifting it outright, plus it remains established through the worst part of the winter and the high winds we tend to get at this point in the year (at least in my area). I have remedied the planting of a tree in this manner in late January without ill effect, though that tree had only been in the ground for about 9mths. Also, our ground tends not to freeze under the snow cover, so I just shovelled the snow back in a large area, did the job, replaced the mulch and then the snow. In spring, I just checked again to make sure that the tree hadn't settled. With the base of your trunk able to breathe, I think the bark should harden on its own. Also, when you plant, try not to add to much to the planting hole, or you can end up creating a 'comfort zone' where conditions are so nice, the roots don't want to move out into native soil. If amending, make sure you do just that, amend the native soil, not replace it. Test your soil to see if it is alkaline, neutral or acidic before adding sulphur, as most JM will do fine on neutral soil as well. Also a good idea to test for nutrients before fertilizing. If you normally wrap your tree in 5A, I would suggest using stakes around your tree and then wrapping burlap around them, instead of right up against your tree. This gives your tree and the all important buds insulation against varying winter temps, where if they are up against the burlap, they are more susceptible to bitter cold and partiucarly warm, sunny days. Sorry this ended up being a book, hope it helps, and if anyone reads this with more experience and better suggestions, please chime in!
Anne

Tha's wonderful information! You can write as much as you like because it means a little less surfing for me. Digging up that little tree was to be Saturday's project but, fortunately, we ran out of time. I'll save it for March and not completely lift it out and follow your instructions to a T. (I can compare results of partially lifting the Shishigashira in Spring to the poor Crimson Queen I had my son raise up by digging it up completely on Friday - glad I had him start with that one.)
Thank you, Anne!