DMBillies, can you tell me how you ran tubing from your skimmer out of your window? The tubing that my skimmer came with is a flexible whitish silicone type tubing. I know that description is highly technical but it is about the best I can do. I would need about 15 feet of this stuff to acheive that and I am not sure how I would deal with the window being slightly cracked at all times. Seems to me that would cause even more issues.
Well, my MRC had a threaded connector for silencing the air intake, so I used some female threaded plumbing parts.
I would just take the tubing you have, take it with you to HD or Lowe's (I actually prefer Lowe's for plumbing options) and find clear vinyl tubing with an ID the matches the OD of the rubber tubing you have... then just jam it inside of the vinyl tubing a few inches. It doesn't really need to be a super airtight seal since there will be no resistance on the air intake side.
I'd recommend creating an air filter to go inline with the vinyl tubing (to help filter the air in case pesticides get sprayed outside, to keep out other air pollutants, and to make sure your intake doesn't suck up bugs or other nasties). To do that, I'd buy a couple of darts that match the vinyl tubing (input and output side of the filter), some adapters to get you up to a 1.5" slip fit, and a few inches of 1.5" pipe. Take some screen and/or cotton balls to line the ends of the chamber and fill the chamber with regular old fish filter carbon. That should help "soak up" bad stuff in the air.
I don't know how often you really need to change the carbon, but carbon isn't too expensive and you probably should run at least a little in your system, so sacrificing some every couple of months shouldn't be a big deal. Just make sure you don't increase the amount of resistance for air flowing through the tubing much at all (really, unless you really compact the cotton balls, you shouldn't have much problem with this).
On the going out the window issue, I just got a small piece of wood, drilled a hole through it that would tightly fit the vinyl tubing, put some weather stripping on the top and bottom of the wood, jammed it under my window, and put a dowel rod between the top of the window pane and the top molding at the top of the window opening (to "lock" the window). This was pretty "rigged", but we kept our blinds closed in that room all of the time because of our TV, so you couldn't see it, the window could still not be opened, we rented so we couldn't go for more drastic options, and it was very cheap/easy to accomplish.
That "fungus" you have is very weird. First thing, fungi tend to thrive in low pH environments, so raising your pH can't hurt there.
I'm also curious, since I do believe your tank is very low nutrient especially if you're using GFO and were dosing carbon, whether you've got any coralline growth? Coralline is a calcifying algae so just like your corals it will not be able to lay down the calcium carbonate needed to grow when the water is too acidic and just like any plant needs certain nutrients to thrive. My guess is, the fungus, which can grow well in a low pH environment is helping to use up what little nutrients are available in the tank. Also of interest is the fact that fungi actually emit C02 as they "feed" instead of fixing it like algae. I'm not sure the extent to which this could realistically be influencing your pH, but it can't possibly be helping matters.
Your clean-up crew doesn't touch the fungus?
Since you've established that it probably isn't algae (and it certainly doesn't look like one to me), again I'd start by raising your pH. Then coralline and other film algaes will have a better chance of competing against the fungus (or whatever it is). If your corals are pale, you might also reduce your striving for a really low nutrient tank. After all, corals and most of the animals in your tank need a certain amount of food to thrive, you're just trying to remove the leftovers before it breaks down and can feed a huge algae bloom. In your case, if you get the pH straightened out you might be able to use moderate coralline growth to compete against the fungus and help slowly reduce the amount of the fungus in your system.
That seems crazy, I know, but my hunch is that you aren't getting any coralline and probably very little other film type algae growth. That could be exacerbated by the fact that everything is covered with this fungus which undoubtedly has a defense mechanism to prevent getting easily crowded out by other species (so those good types of algaes don't have anywhere to settle and get a foothold). So... what I'm really proposing is a balancing act... which is really all any of our tanks are. Not all algae growth is bad and coralline is especially desirable because it prevents other nastier algaes (like hair algae and hopefully, for your case, this weird fungus) from being able to settle the substrate.
Edit: If you're blowing a fan in your window at night and not seeing an increase in pH relative to nights were you aren't (you need to test at the same time), the c02 in your house may not be the problem. I'd recommend the cup of water trick I talked about in my blog. Test your tank water in a cup, walk outside, stir the water really hard for a few minutes, then walk back inside and test the pH again. It would be even better if you could do it in the morning and at night. That will give you the best indication of how much you can expect your pH to rise as a result of outside aeration. In my case, it was a pretty stable .2 regardless of the time of day, which is fairly significant...