Wanted to add on to this. I also purchased 1/2 by 3/4 silicone tubing from the brewing supplier that OP mentioned and when measuring the pervious tubing it came out to 8-5/8" so I cut both tubes to that length and ground the two flats to the same size as the origional. A flap disc on an angle grinder worked best for me. The origional flats measured around .610"-.615". I kept my tolerance around +/- .005. Installing the tubing was indeed tricky due to the large wall thickness but with some heat and elbo grease I was able to install it all back together. When screwing the hoses back in I made sure that they were both sticking out the same length.
Once everything was installed I started it back up and it still did not want to move. While messing around I got it to a position where it finally did start moving but eventually I went back, disassembled the entire unit again. This time I had cut the tubing EXACTLY at 9" and did not grind any flats, installed it, and viola! The MM was working better than before. I think that missing bit of length was the issue as before it didn't create that "snap" when the hose flexed from one side of the wall to the other and as for as I'm aware so far the flat spots are not needed?
I am still facing an issue where most of my jets need to be closed for the moto massage to work. Fingers crossed I don't think it's an issue with using an aftermarket silicone hose but instead an issue with water pressure. I don't think it's air pressure because I have blow out the air line with a compressor from both the MM end and the air control end and ran the MM with the air control valve off and still behaved like before. I have also tried running it with the filters removed. No luck. My best guess seeing as this is a 2013 Jetsetter is that the wear ring is worn and since I have rebuilt the entire wet end except for replacing the wear ring I think that's a good place to start. Anyone else have any ideas what might be causing the issue?