That is a tragic story, indeed! I have done this very procedure many times, so have courage. You can go about this two primary ways: the first is simply to repot the entire tree; the second is to cut off the healthy top and root it, and also repot and hope the trunk and rootmass survive. I think it is imperative that you use a free-draining potting mix. I use bark, perlite, lava rock, and just a little potting mix as a binder/moisture retentive ingredient. And when I say "a little potting mix," I mean less than 10% of the overall mix. If you can't mix your own, I recommend a fine-grade Orchid Mix, to which you will probably add some coarse Perlite. Repot keeping the roots moist at all times, thoroughly water and saturate the new mix when done, and place the tree in outdoor shade if available - no direct sun. Keep the mix uniformly moist with light waterings for at least a week after repotting. You can either repot the tree first, and the cut the top off....or you can cut the top off and repot the tree all at once. It's a bit of a gamble, as I don't know the vitality of the tree, but I have confidence from repeated experience that the top will root (if it is healthy as you describe). I place the cut top in a vase/jar of water, and I wait for white root primordia to appear. As soon as they appear, I transfer the cutting into a container of the same moist, free-draining mix, and I keep it moist while the cutting continues to root. I use #1 nursery containers.

On rhododendrons, peeling bark is normally a highly prized attribute. For example the R. barbatum on the left and the R. maddenii on the right are well known for their peeling bark. However, it can also be a sign of problems such as with Botryosphaeria dieback below on left and bark split on right. Dieback is often caused by drought and only affects several branches. Bark split is caused by a warm spell in winter which causes the sap to rise, followed by a heavy frost the freezes the sap and splits the bark near the soil line.

pika Where are you geographically? A couple of those pictures look like a gall growth of some kind. And they can happen on tomatoes, though that's very rare. Most of the internet sources mention its existence in the UK, on grafted tomatoes in greenhouses. See below. I have to agree with others that those don't look like tomato stems or leaves to me. Maybe it's an unusual variety? Here is a link that might be useful: Tomato -- Crown Gall

EDIT: I finally found an answer to my own question. Apparently, these bumps are called extrafloral nectaries, which secrete sweet nectar outside of the flower to attract pollinators. Ants are commonly attracted to these bumps, which can also appear on the outside of buds. The presence of ants, as annoying as they are, can help the plant by keeping pests and fungi away. So, don’t stress about the ants unless they are farming and milking aphids; the flower drop is probably unrelated and due to nitrogen in fertilizer, which promotes leaf and vine growth but inhibits fruit production. “Did anyone ever find an answer for this? My passion fruit vines show the same bumps on buds and stem of leaves, black ants attracted to the bumps, and flower drop, even when hand-pollinating.”