First contact Krash and see if they will help. With them trying new things they will want all the positive light they can have in the market so you might have good luck. If that doesn't happen for you or for short term then do it yourself, which you will probably end up having to do in the end so might as well just prepare for it lol.
I would do as listed above and try the silicone testing. Get a Watcon or another big bulky good seal and use that. On the under side of the hood I would get a carbon fiber kit and lay up a few layers on the sides in the valleys and then shape it down with a block sander till its all level. But I would make sure the hull side is level as well because if that has valleys than a new seal I wouldn't see help you there. I had a Backie chan and only used the ratchet strap, I'm sure you would be fine with that as well. Maybe use the buckle straps (the ones Jetmaniac sells I believe) as well on the sides of the ratchet strap for surf days just to be extra safe. The latch is always nice since it is a bit quicker but sitting on the side getting the water out of the ski looks to be taking some extra time too haha. You aren't running a kart or Jazz tank so you don't need to be popping on and off the hood as often as you are right now. I'd do whatever is the quickest and easiest for you the rider to get you on the water and keep you happy.
Yes, I sent Chris a message asking for a hood to start with a proper sealing surface. He has been helpful so I have hopes we will be able to work something out. He probably reads this thread to keep up with PR, as well as any other Krash related threads on this forum. I'll see how that goes and move in a direction.
Are you running stock air boxes?
2 things causing this.
1. You are not putting your hood in right. That gap is massive for how it should be.
2 . That ski is licoriceed up and you should ask to trade it for a prebuilt one coming out.
I've had water get in my engine since the beginning and that is why I switched to the stock 760 intake. The first two rides had flame arrestors, the last ride I had the stock 760 intake.
As the photos show, the ski side bows down slightly in the center from the corners and the hood is visibly wavy/bowed without a straightedge.
The hood cannot flex that much either so incorrect installation is out, and the corners are firmly pressed into the seal while the centers have gaps.
Nothing is pushing on this hood and look at the dips. You can't tell me that is user error.
Just a susgestion, why don't you rip the hood seal out and do the pour in silicon seal that tigercraft is doing. 
Here are 2 pics of mine.
