Some thoughts for you
Based on the plans you've shown, it looks like you want the ability to have a continuous run, as well as some sort of reverse loop. You also seem to favor an almost random assortment of spurs and sidings going every which way.
Variety is the spice of life, but sometimes things can be too spicy to enjoy!
First and foremost, let me say that it is your railroad, and you can and should do whatever you like. With that said, there are things you might want to consider which could help in making this a more positive experience for you. You seem to be assuming, and even expecting, that you will have an utter failure on your hands, and I feel strongly that is a poor approach. The first time you hit a stumbling block, you will be tempted to give up, since there's no point in wasting time on a failure. Why not do the very best you can, see what happens, and know that you will learn things which will be helpful for a future layout, while still enjoying this one?
While a model railroad is a personal thing, and of course some fads are just that, there is a lot that can be learned from trends and conventional wisdom. Many of us have done the "every piece of track that will fit" thing, along with the 4x8 thing, the giant loop thing, and a variety of other "things." If you chose to go down that road (and by all means, feel free to do so), at least consider what others have to say about it and make the decision with open eyes. I will also say that, without exception, every time I have said "I know how to make it work, and those guys just don't know what they're talking about" I have lived to regret it.
As has been pointed out, 39" deep benchwork is problematic. You will not be able to reach across it, and I suspect that you will get tired of having to pull the layout out and walk around it. Depending on how high it is, I would not put any turnouts closer than 18"-24" from the front edge. My benchwork is 50" high in most places, and ranges from 16"-18" deep. It is comfortable for me to work on, at 6'3" tall, but I would not like it any higher or deeper. I also do not like layouts that I have to walk around to access, because unless the throttle is completely wireless, sooner or later you're wrapped up in or at the limit of reach of the cord. I prefer to stand inside the layout and so access every bit of it comfortably - not glued to a single spot, but not having to go around obstacles to reach.
On to track plans! The big issue I see with the WR&N is that it requires some fancy expensive or custom track work - especially curved turnouts and crossings. It looks great, but I suspect it may not be right for a first layout. Your first plan actually looks easier to build, since it's made up of off the shelf components. Also, nixing the staging yard on the WR&N is, I suspect, a mistake. It seems to me that a lot of the operation on the layout is dependent on running several trains in a variety of routes, but without the staging yard you cannot easily have that variety of trains.
I have often suggested that a short line or branch line is the ideal theme for a small one or two man layout. Large, busy main line operations are impressive and make magazine covers and articles, but they are difficult to pull off without a good bit of space and manpower (or a lot of automation, which is impressive to watch but boring to be a part of). With a little care, it is possible to achieve a good mix of industrial, city, and rural operation in a space like yours. For example, here's one track plan I cooked up in HO scale for a very similar space:
Would you be interested in seeing what others might come up with for suggested track plans? Or, would you prefer to develop your own, based in part on advice and inspiration from others?