I had an older fishcat, which would be a fishcat 8 now. Can help you quite a bit.
You really don't need anything to cover washers and frames to protect the pontoons. You can, but for most part your frame should be strapped down tight enough that no rubbing will occur. You can glue chaffe pads to the tubes, that would help the most actually. All you'll need is some waterproof glue (usually found at sporting goods and can be bought from manufacturers like Aire, Sotar, Wing, Skookum, etc) and then buy some protective vinyl to glue to top of tubes. You can also go directly to outcast to see if you can buy a piece of bladder material wide/long enough to cover where the frame will rest and then glue it down there. This is your best defense.
Onto accessories. I actually don't like verticle rod holders UNLESS you don't drift down brushy streams or only plan to fish lakes. Only reason I say this, is that anything sticking above the rower, or outside the length of the boat is susceptible to damge. Only takes a second to have a rod get grabbed and snip a tip in an overhanging tree. Or have a quick hit on rock/limb while maneuvering a chute and have boat miss the object, but your rod tip nail it. I wish I had pics of my old fishcat modified (or my pac model in fact). I did alot of work to make mine fishable. What I'd do, and will see if I have a name for them, is buy rubber rod mounts that can hold 4 rods. The drill right into the frame. It's what I had on my outcasts. What this does is keep the rods on top/near side of frame. I found it's best to take a few seconds to take a rod down (if it doesn't fit inside lengths of your boat) and put in one of these rod holders then to chance ruining a days fishing (and a good rod) by trying to save an extra few seconds to take a rod apart. Now, I'm set with my 16' cataraft. :hehe: Unless I start using one of those 18' Daiwa's that Fred uses, I'll be set.
But I would actually take my rods down on my 9' Steelheader. My 14' spey I would only take down the tip section and would be fine. Like I said, rather take a few seconds to take down then to chance snipping tip off.
For storage, there is a cool new bag that Cabela's sells that actually sits on your chair and can toss stuff into it behind your seat. Should still have room for a cooler too. I'll see what I can do about getting pics of that rubber type rod holder. I know a local sporting goods store carries them here in WA (actually, think two do). They worked great for me. Plus, the rods won't move while in them and are protected.