Well, I thought about it a lot. Had a friend come over and look at it and we agreed that the boat would be much mode practical without those frames.... I just cut them out. It looks much better and it is a lot easier to work on.
After thinking about it this is what I decided on. I cut out the light blue portion of the frame. I will add a third batten either side of the hull just inside of where the old frame was cut off. I will add small frame that will span over the keel between the 2 inner battens (orange). The keel, batten and chine logs will get a fillet of epoxy on either side. The chine logs and keel will be taped with glass. I will create a sandwich with an inner floor of 1/4" plywood covered with glass. This idea came from Eric. I think it will be very strong. The only weak spot maybe where the new batten butts against the old frame. I could not figure out how to join them (area in the circle in the diagram). I removed 4 frames and they with be replaced with 8 of the smaller frames/braces along the length of the keel.
I think it will make a very clean strong hull. Little hard to clean the mud that will collect under new floor. I'm committed now!
A bold move my friend but I totally get the desire to unclutter the interior. With 4 oz cloth glass the hull interior and both sides of the 1/4" ply floor. You are not far from creating a torsion box which are very rigid. In fact if you were to bond some batten thick pieces in the opposite direction, say where the frames used to sit, you would be creating a torsion box floor structure. Further, if you glass in some plywood knees into the frame gussets that notch into the battens and then have the floor notch into them you will lock everything together. I wish I had your computer drawing skills so I could make a diagram to compliment yours.
Another look. I'm not sure you need the new batten. The knees will tie things together. This picture and the above show no new batten. I'm not sure it is needed.
Don't cut your drawing skills short - I cannot draw in 3D. I thought about leaving part of the old frames to allow a means of attaching knees like you suggest and end up rejecting the idea -- maybe too soon. The added batten is required to support the plywood at their edges. I also thought about putting those cross pieces between the battens, but I don't want to trap water between the floor and the hull. I was not planning to run the floor under the side decks. Instead of adding battens, I could run them along either side of the gussets and stop them an inch or so from the battens. Then extend the floor under the decks. Maybe making a few holes along the other edge of the plywood to allow air flow. The floor could be attached to either side of the gussets with fillets. I stuck a piece of plywood along one of the gussets to show what I mean.
This would still allow enough space to store decoys under the deck.
The floor in my Black Brant is bonded all the way around the perimeter. The plywood runs under the decks and tapers into the hull. It is epoxied and glassed. For access I installed screw-out deck plates. The below pic from a recent refurb is the best I have handy. The tape is to keep paint off the GI bed mat on top of the plywood floorboard. One of my hunting partners goes over 260 and he broke a deck plate. I epoxied a plywood "platter" inside the lid to keep that from happening again. Grit can get in the threads making them hard to unscrew. They make pop-out versions. Other folks have used plywood covers with magnets to hold them in place. A nice solution.
Getting the plywood floor shape wasn't hard once I figured out the method. Basically I cut similar pieces of wood (1x3s) and set them 90 degrees to the keel one foot a part. Once they were centered and all lined up along the keel, meaning a straight edge would touch each of the sticks, no gaps, I had the shape of the floor. I transferred the sticks to my ply which had a centerline marked, traced the resulting curve using a flexible batten, and cut it with a jigsaw. Very simple and quite accurate.
I know your floor isn't flat all the way across, but you should be able to do something similar.
Eric - I was thinking about your advice to install "knee braces" all day yesterday and then I got your new post. I think I will follow your advice and figure you how to install them. I went back though your post on building the Black Brant to see how the floor was supported. I'm just thinking aloud now. I've sketched up a couple of options. This one would be easy, The only issue is I will not have gained much depth -- but it could be a good compromise
If you look at the photo in my last posting with the closeup of where I cut the frame off you can see that there is a place between the gussets where I can insert a knee brace. I'm just not sure how you get the floor inserted into the braces. I wish I could take you up on your offer and hang out in your shop and talk it out over a beer. But the forum is good - thanks for sticking with me.
Here is another shot of how I did my floor. The floor itself is notched into the knees, which are actually cockpit bulkheads. By filling and glassing the notched areas you lock everything together. Also, I used 1/2" ply on my floor. Any thinner and it would flex too much.
In your drawing above you could gain a little more depth by routing a rabbet in the batten and having the plywood floor butt into it. It looks like your path to route that rabbet is clear, plus that gives a firm place for the plywood edge to land and withstand weight of foot. Don't worry about perfect joinery and odd angles. Epoxy mixed with wood flour will fill the gap. Lastly, I'd not have the knees taper into the floor. You want some meat there otherwise it will be a weak spot. I think you want to tie the knees into your new floor supports. Even if they protrude above the floor a bit in places I don't think it will bother you when walking around.
Don't fret. I know you'll see a solution. I think you are close to it. If we were standing in the same place and seeing the same thing sawdust would already be in the air.
I wish my hull looked like that I've been in the garage all morning making sawdust. It is much easier to fix mistakes with the computer than the bandsaw. But I think you have it now. I can carry the knee out to join up with the new floor support. I could also set the floor support just in front of the knee to allow them to be tied together along their sides. Following your suggesting, it would be good to let the plywood floor into the knee and I think the rabbet is good idea -- even a 1/4" rabbet where the knee or floor support crosses a batten to the keel will make a more secure connection.
I've used up all my scrap pieces of MDF... and managed to make a mockup of one of the knees. Unfortunatly the boat does not appear to be perfectly symmetrical. I think the hull is, it is just the angle of the plywood gussets is a little different on either side of the boat. No big deal for the boat, but the pattern needs to be adjusted a bit. But maybe just fill with thickened epoxy.
Just to be clear my idea for the rabbet was to allow the plywood floor to sit lower. If you rabbet the entire length of the batten the thickness of the plywood you make the cockpit deeper by 1/2", which may or may not be worth it. You latest picture shows the floor with a feather edge on top of the batten. A little different but that is similar to my Brant's floor construction. I made that edge with a block plane. Since your battens are straight you might be able to cut it on the table saw by standing the plywood on edge.
I've been in the garage all morning making sawdust. It is much easier to fix mistakes with the computer than the bandsaw. But I think you have it now. I can carry the knee out to join up with the new floor support. I could also set the floor support just in front of the knee to allow them to be tied together along their sides. Following your suggesting, it would be good to let the plywood floor into the knee and I think the rabbet is good idea -- even a 1/4" rabbet where the knee or floor support crosses a batten to the keel will make a more secure connection. 
