Well, it took most of the day but I got it changed out. Would have been a really extraordinarily simple job except for the fact that the water heater had been cozily installed under our kitchen counter. At first I didn't register exactly how tight the space was (deceivingly large amount of space between the top of the water heater and the bottom of the counter) so I'd gotten a unit that was an inch-and-a-half too tall.
Returned that and got the proper size only to discover that it was still too tall due to the old unit being about an inch shorter in total height due to smaller pipe connections which were also slightly sunk into the tank (the new one had longer pipe connections flush with the top of the tank). There were no smaller units unless I wanted to go with a tankless or a point-of-use tank so I improvised and got a couple elbow bends- which changed the angle of connection enough I was able to get it under there without too much fuss.
Apparently this brand, being different from the old one, had a slightly different water input configuration, so I had quite a time getting the pipe to it on and connect to the house line. Had to twist the unit so the thermostat and drain were almost facing the back wall. I'll probably need to fix that at some point but it was getting later than I expected so I had to make due for the moment.
Copious use of teflon tape, happily discovering that one of my wrenches has about a 15 degree different grip angle than the other (allowing me to tighten bolts in tight spaces), and a good amount of testing for leaks and I'm pretty sure now I can call that project mostly done. At the very least it's done enough that I don't have to worry with it for another year of two when I flush the tank like I should have been doing all along :)
Also the mold, or whatever it was on the water surface, ended up being a non-issue. I'd put some bleach in the standing water a few days ago and when I actually got to the heater exchange it looked a lot better. More I think about it more I think I was over worrying with the general levels of stress going on at that time. Just have to take the old one to the recycling place now.