RE: tuned pipe
What they are telling you is that if the header extends inside the pipe, it changes the way the pipe works. You need to cut the header so that it's exit end is approximately in the same location as the inlet end of your tuned pipe. I would recommend moving the pipe back out to the end of the header and run it on the water and then start cutting it off a little at a time, running the boat so that you can monitor how the engine reacts to the changes under load