here is the problem with your current setup. the water streaming along the hull (blue line) is high pressure. at the intakes, the pressure lowers due to having more space, just in front of the intakes (green). it will have even lower pressure there because you are sucking the water away. in short, your waterjet will lack enough water when at speed, and will thus suck itself dry in the current config.
so, the intakes must be at the keel level, or you should have the hull move up in a curve instead of in a single large step. it is better to have an short tunnel (both from internal space and from resistance viewpoint) so you might want to experiment a bit
also. this ship has no planing or semi-planing hull. that means that you have an speed of max 34 knots, which is about the maximum efficient speed for propellers as well. LCS-1 and LCS-2 are a planing monohull and semiplane trimaran respectively, with an top speed of 50 knots. while they are about the same size as this ship, their role differs a lot.
note that waterjets are inefficient on speeds lower then 20 knots. most sonars work best in the speed range between 18 and 20 knots. I have to admit I have no data out of the top of my head on towed arrays, but I would say this would be the same. so, when you are planning to operate your sonar for a long time, you will operate under inefficient conditions.