Yep, like Lucky_Chicken said, you can orientate this system anyway you want since your are forcing air/steam through an Open System.
Unfortunately klyph, I think that the setup that you mentioned is a Closed System. A closed system like this would require a higher pressure within the piping to 'break though' the water, kind of like when you blow bubbles in a glass of water with a straw. I think the difficulty with this system is that you would need a fan that is capable enough to create this higher pressure - this would be a challenge with my setup since the range fan is just powerful enough to push the vapor through open tubing. Now you may be able to do this is you had a lid that sealed onto your pot, a la pressure cooker. Then you wouldn't need a fan at all.
But as far as I've read and understand, its best to whisk away unwanted boil-off/vapor as it prevents DMS from getting back into your brew. That's why I'm thinking that an open system is maybe the best since it will have a reasonably higher flow rate.
Oh! I did forget to mention with my setup that I did position the Stage 2 heat exchanger like that for a reason *Steam comes in at the top and exhausts at the bottom... I am feeding the cool water from the bottom of the Stage 2 copper pipes, reason being that I want to have even distribution of cool water traveling up the pipes. If I fed cold water from top, the water would just fall down the copper pipes, and most likely only through a few pipes instead of evenly filling all of them at the same time. Also, this creates a counter-current method of heat exchange, which is most efficient, being that the cold water flows one way and the hot vapor flows in the opposite way.
So, if you just flip my system you will have to feed the water from the top, which isn't going to be as effective. But with some changes this can be solved. Maybe the cross over pipe can go from the bottom to the top, so instead of an " U " shape (my system is an upside-down " U "shape) you can make an " N " shape. But like I said before, there are many ways to approach this.
If you can just easily run a fan through your wall to the outdoors, I would definitely recommend doing so (like most people do). Its by far the easiest to do. I would only be considering the steam condenser method if you are stuck in a spot where you can't directly or easily plumb your exhaust outside.
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As an update, I did another brew this weekend and used the steam condenser system again. I again was stuck with another situation where I had to boil-off a lot of liquid, but the steam condenser just gobbled all the vapor up. Once I was able to run the boil at a normal light rolling boil I saw a reduction of ambient temperature to a very comfortable level. I expect that once I get my liquid volumes dialed-in so I don't end up having to boil-off over 2 gallons in 60 minutes, I will have a very efficient system and only see a slight increase in ambient temperature.
Also, I made a 'quick fix' for extending my range hood lower to the pot. I took a tea towel and two magnets (left over from making my stir plate) and fixed it to the back of my range. It greatly improved range and its ability to capture all of the steam - I would say 99% now. Also, the tea towel seemed to catch many of the rouge-drops that collect and fall from the range. For now I think I will stick with this until I think of something better.