I'm not at all sure your tree needs any saving :-)) Doesn't look like much wrong with it to me. I'd want to see a clearer view of the base to make sure the root flare was obvious but best as I can tell from photo, even that looks OK. Discoloration of bark is normal and attributable to both sun/shade conditions and the development of some harmless lichen. The yellow stuff is certainly a form of lichen and again, harmless.

I can't see clearly but are there holes in the foliage or just spots? Spots are not an indication of insects but reflect uneven watering of the newly planted tree. The soil should stay evenly moist at all times, neither too wet or too dry. If insect holes, that is not much of an issue either. And since JM's resent having anything other than water sprayed on their foliage, not much you can do about it anyway.

Seriously, I think you are worrying unnecessarily.

The leaves look like a little wear and tear.
The depression on the trunk worries me. It looks like the cambium layer is dead under it and it will just be a matter of time before the bark separates from the trunk.
Maybe not, but it bears watching.
Mike

Thanks guys. Here are some more pictures.

First picture, is a better picture of the crack, or cracks rather, it's kind of a depression I guess..

Here is a pic of the other side of the tree.

The bottom 6 or so inches of the tree has always been somewhat darker, I suppose because of the graft location? It looks even more contrast in this picture, because the tree/bark are wet.

Lastly here is a picture of the overall tree.

Thanks guys!

As gardengal wrote, the leaf spotting is a result of water stress and is not a huge problem. If you want to go to the trouble, expanding the mulched area around the tree would be a good idea. Turf grass consumes a tremendous amount of water and is competing with the maple. Emperor can eventually become a large tree, but will have a lot of difficulty expanding its root systm into areas of dense grass.

That damage on the trunk is alarming. I'm pretty sure it will develop into a larger, open wound during the winter. Next growing season will determine wether the tree will be able to handle it or not.

Can't I wrap the wound with something? What would cause something like this?

I'm thinking either it was planted too deep or mulch was/is too close to its trunk. (click on photo)
source: http://hyg.ipm.illinois.edu/article.php?id=274

Dax

I can certainly remove some soil from the base, maybe it is planted too deeply.

The sunken area at the base appears to be to be canker. Had to remove a Ukigumo JM earlier in the season for this very reason. I have seen allot of this over the last few years. Have seen allot of it on crabapples, Japanese Maples, and other maples. Plants sometimes beat the pathogen, sometimes not. If they are going to beat it, then expect to see callus to form around the edges of the sunken area. Even if the callus forms, it is far from certain. Once the tree goes dormant for the winter, the canker will often gain the upper hand again. However if the callus does not form by end of summer, then from what I have seen, it's almost certainly a matter of time before the tree is killed.

As for how your plant became infected, I suspect that a number of low cost and/or large scale producers have gotten very careless over the last 5-10 years. There has been allot of apparent disease increase in allot of other plant groups as well over the same period (Aster Yellows seems to be everywhere anymore, to the point it's getting rather difficult to get disease free coneflowers, saw this Saturday at the largest local nursery). I'm sure part of it is due to producers having a difficult time the last several years, therefore cutting corners, poor training, poor enforcement, less responsible labor, etc. But also Big Box Store has little incentive, as they know Q Public is unlikely to know anything about disease and will be back again next year to buy another one.

Arktrees

Thanks guys

Hmmm....Went to a few garden centers. First guy said JM don't get cankers and to just wrap the wound with electrical tape for 2 years, it will grow with the tree, then remove it. I laughed and said OK.

Second lady said it looked suspicious and might as well return the tree since I can.

Just like anything else, it seems if you ask three people about it, you will get three answers, lol.

The place I bought it however has no JM's in stock. They should come august early September though so I guess I will wait until then.

Sucks, because I love the trees structure and shape.

So...I was inspecting more today and brushed some dirt away around the base, when I did this I noticed probably a hundred tiny ants. I then noticed there was quite a few in the mulch too. Odd. How can I kill them without harming the tree. Keep in mind some are like under the mulch.

Any other thoughts?

Don't worry about the ants - they are harmless. And JM's certainly DO get cankers but that mark on the trunk looks nothing like a canker. Is it soft and spongy? If still firm, it could be as Dax said and just the result of mulch piled against the trunk or even some mechanical damage. And, JM barks is very thin and can get damaged for all sorts of reasons, most of which are nothing to get overly alarmed about. Regardless, put NOTHING over the area - keep dry if possible (no directional irrigation heads hitting the area) and allow the tree to do its thing.

gardengal,
I have seen several cankers that looked exactly like that on JM locally. Cankers are simply sunken areas, and are not always spongey. Now in this case is may not be canker, as one can never tell for certain from a picture. But I have seen this same appearance many times, and when I looked very closely, would find that there would be dark/black areas just under the outer bark. Whatever the pathogen is, it seems to attack the cambium leaving the bark above, and the harder wood below intact. And since a rather thin layer is destroyed, there is very little to no softness in the sunken area.

I did not put this in my earlier post as I did not want to unduly raise expectations for the original poster. The cracked edges of the bark on the edge of the canker suggests that callus has formed and that the tree is winning, at least for now.

JMHO
Arktrees

That sunken bark is of considerable concern. To my mind, it's a huge wound and a relatively old one at that.

As has been suggested, it's a good bet the overlying bark begins to flake off next year.

I'd follow the advice to have the tree replaced while you can.

As for the guy who suggested the electrical tape, please locate a more knowledgeable source of info.

Thanks guys. I suppose I will replace this tree. I will most likely wait another month, hopefully the place I am exchanging it gets more Jap Maple Emperor 1s in stock.