I hooked it up almost exactly as you think -- with flexible hose between the hood and the airbox. As far as a step-by-step, I just about gave it to you above. Just pull out the stock air inlet tube, saw a hole in the box where it went, and stick in the fitting for the flex hose.
Run the flex hose to a spot where there is room on the bottom of the hood, hole saw the right sized hole, stick in the fitting for the hose, silicone everything in place and cover it with the scoop.
I think it took me less than an hour to do the entire job, start to finish, incuding pulling the air box. It is very simple and it works.
Water is no problem. It runs out the holes drilled in the bottom of the air box. Also, a bit of water in the air stream won't hurt an engine -- and can actually give it a boost. Just ask any old drag racer that used water injection.
Anyway, I've never had the slightest bit of problems with water. After all, even the stock front mount breather hole sucks in water when running in the rain. Just normal for most engines. At least my design lets it run out of the box if it really gets full.
About the flex hose cracking, yes, I guess it can and likely will. No biggie... That stuff is only about $9.00 for a 10 foot piece. You get three runs out of one piece, so for $3.00 I can replace it if it cracks. So far, I've run it for almost 2 years with no cracks, so it is holding up very well.
Again, it is RV flexible poop-tube.
Here's an example of what I'm using -- works PERFECTLY (no recommendation for this particular site -- just a reference)
http://www.pplmotorhomes.com/parts/rv-toilets-tanks/heavy-duty-rv-sewer-hose.htm
http://www.pplmotorhomes.com/parts/rv-toilets-tanks/sewer-hose-fittings-ez.htm
Here's the hood scoop:
http://cgi.ebay.com/ebaymotors/Blac...9QQihZ002QQcategoryZ33646QQrdZ1QQcmdZViewItem
If I get a chance in the next day or so, I'll snap an under-the-hood picture to make it more clear.
Oh, and I do get that thing in the mud/water...
Saved my bacon this day... As you can see, I was in over the top of the grill before I came blasting out the other side. Another participant spend an hour sitting in this same hole, with water up over his engine, flooding it and filling it... He ended up rebuilding everything.
I lost the fan clutch and water pump from plugging the radiator with mud and crud, which sucked the bearings out of the pump, plus killed my fan clutch. The price of wheeling... But, no mud in the air box.
With the stock intake, I would have been dead.
This is what I see out the windshield: