Definitely too flimsy. I haul canoes and would never rely on friction clamps to hold a 5 foot lever holding a kayak at highway speeds. There is too much bouncing around by the trailer not to mention the kayak wanting to move side to side in the wind terbulances as well as front to back and the front and rear uprights not being connected together at the top. I think the clamps are going to wiggle loose just from the kayak wanting to move around.
You might try this
Side Load Kayak Carrier. Although made for a Little Giant utility trailer, it has brackets at the bottom that can be screwed or bolted to your trailer floor and the kayak supports can be rotated to hang the kayak inside the trailer. At 6 foot wide that should give enough clearance for the motorcycle. You can also add u-bolts drilled through the side of the side of the top angle rail on the trailer to hold them vertically. Loading would be way easier than lifting over your head. You could also use a split pool noodle to pad the kayak to keep from scratching it on the rack.
If you still want to use the pipe you already have I wold recommend adding
1 inch threaded pipe flanges cutting the edge off one side of each leaving them kind of D shaped with 3 holes left and using screws or bolts to attach them to the trailer floor. Then using u-bolts bolts as mentioned above to attach the pipes to the top angle on the trailer sides. The D shaped flanges will allow closer fit to the side rails. You'll still have to lift the kayak over your head to load it.
For loading my canoe solo with a Yakima Rack there was a a loader bar that had a flange and slid inside the Yakima Rack bars. I didn't want to spend what they wanted so I got 2, 4 foot threaded pipes that would slide inside the bars and added a matching pipi flange to one end on each. When loading and unloading I pull the bar caps on the sided I am on and inserting the pipes with flanges into each bar and I can then lift one end of the canoe up flipping it over and resting it on the pipe. Then I lift the other end and then rest it on the other pipe. After positioning the canoe and tying it down I removed the pipes and put the bar caps back on. The flanges kept the canoe from sliding off the pipes when loading and unloading.
You might be able to do the same by changing one or both elbow on each of your uprights with pipe tees.
Don't forget to use something like a split pool noodle or foam pipe insulation to pad the kayak and keep it from moving side to side. You will get some movement with the 2 uprights not being connected together.