The cowls have water drains and stock air filter housings have water drains as do ATS turb o air filter housings . I was a bit concerned at first, then I ran pulling my carhauler through the most insane frog strangler I've ever been in where it was coming down so hard big trucks were down to 15mph on the interstate and most had pulled over due to lack of visibility, and I kept on plugging and when I got in , I right off the bat pulled the air cleaner open to see if there was any water in there and it was bone dry, so I'm not the slightest bit worried about water. Only thing you have to really keep in mind is heavy snow. If it's going to be snowing enough to block it off, you need to pop the hose off or you will be drawing air from inside the cab and your heater won't work ( the vacuum from that engine sucks a heck of a lot harder than that poor little squirrel cage fan can fight against for air when the main supply gets cut off so it has to come from somewhere )
I really love my hypermax setup. If you try to make your own, the biggest problem I see will be matching teh shape on the firewall. It's not flat there. I'm sure it can be done with sheetmetal and a lot of sillyscum to take up the irregularities. THe preformed plastic piece that Hypermax has makes it all so nice and simple.