The bronze coloration in the fall is a trait of the plant and is sought after. A high water table is bad, very bad. It is best to plant in a raised bed in such a situation. But the problem you see doesn't seem to be acidity related or root rot. Low soil acidity causes chlorosis, yellowing of the leaves between green veins. Root rot causes general decline of the entire plant, not just a couple branches. The dieback you see can be caused by borers, or by a summer drought or even some roots in too wet an area. It is best to remove the dying branches and destroy them. If the ground is too moist, replant in a raised bed. Here is a link that might be useful: How to care for rhododendrons and azaleas.

I left out Gnetophytes, mostly because so much of the evidence seems to be contradictory. Most genetic analysis I've seen suggest Gnetophytes aren't all that close to either other gymnosperms(conifers included) nor angiosperms, but branched off from other gymnosperms well before the split between angiosperms and gymnosperms, while most morphological and fossil evidence seems to suggest an intermediate position for Gnetophytes between angiosperms and other gymnosperms. I will say, I haven't read any genetic studies more current than about 3 or 4 years old though. Good point treelover2, both Sciadopitys and Ginkgo are quite old also. But from recent studies Ginkgo is no longer considered a conifer, but it's still a gymnosperm. The latest I've heard is that Gingko is more closely related to Cycads than to conifers. But nobody has addressed which living genus is the oldest conifer? I've also heard that Cedrus has been shown to be basal in the Pinaceae which is basal to all other conifer families(basal within Pinales). Is this the current thought still or is it something else?

No-Clue I took my clues from the neighborhood also when I first tried putting the plants in the ground. Lots of them in my area (Glendora) and there are many really big ones out there. In Hawaii, there is very little real dirt. Most dirt is an inch or two thick and then lava rock. One place I know doesn't have any dirt at all. Just lava rock. And there's dozens of plumies by the side of the road. Plumeria thrive in Hawaii growing in rocks. Here's a shot I took in 2008 in Hawaii. This is new land, only a few years old. Look what's growing. We're headed back to Hawaii next month and plan to go and try to find that tree. Got the general area, but there's about a mile of what you see above. Nothing but black lava. Kind of hard to pinpoint a location. It all looks the same. Acres and acres of it. It is by a path though. I figured if one can grow there, I can grow them in my crummy dirt I have. So I brought a bunch of them home, rooted them and then stuck them in the ground. No amendment, no topsoil, no compost, no nothing! They're doing wonderful. If they are rooted, they will grow. Good luck.

there are enough white roots to attemp recovery. but, there are dark-brown roots here an'there - that's the rotten roots.. they are very soft and you can just remove them with your fingers, they'll fall off. you can try then fine cutting with small scissors to remove all brown looking roots. and you need to soak the root ball in some disinfecting solution with alcohol (like 9:1 water with rubbing alcohol) or 3%peroxide with water solution (1tb per 1qt) for 5-10 min or so. after that i would plant in 100% sterile perlite for rerooting/recovery. no soil-mix until it starts growing (IF it doesn't rot more), then you can repot. make sure the top cut is clean - no dark spots. you already cut it, but generally i'd cut an inch below any rotting signs in the cross-section.