Get ready to read a long response with all your questions answered backed by 20 years of welding, fabricating and coating experience
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Powder coating is and isn't the solution, note pretty much all frames come from the factory powder coated and how are they holding up? The problem with most frames made out of steel and aluminum is that they do not seal them up completely so water will get inside and corrode the frames at the joints no matter how great a coating you put on the outside it's going to corrode on the inside. Not to mention they are using the thinnest wall material they can get away with.
Powder coating is great and I use it on alot of stuff but it cannot get into all of the crevices at weld joints and any where you get a chip in the frame rust or calcium will begin to develop and travel under the powder coating.
Also alot of powder coaters will go the cheap route and not sand blast before coating if you bring them something that is bare metal, do not use these people because they suck... any good coater will blast anything and everything before coating.
Here are you options.
1. Take your brand new frame and have it sand blasted, then have a welder seal all welds and openings in the frame so it is water and air tight and then have it powder coated.
2. Same as choice 1. except before you have the frame powder coated get it metallized "http://zincnation.com/" see link for what that process is. Some serious corrosion protection and rust/calcium will not travel under the metallizing.
3. Take your new frame to a place that does spray in truck bedliners and get it coated for an extra beefy layer of protection.
4. Probably the most expensive is to take your frame to a welding/fab shop and tell them here duplicate this out of stainless. The stainless itself will never rust but be warned metallic particles in the air and water will stick to the stainless and cause rust spots. Most can be cleaned with a stainless wire brush or scotch bright but never ever use steel/copper/brass wool to clean stainless. With proper care that frame will outlast you and all the pontoon bladders you can throw at it.
Hope this helps and gives you the answer to your question