That's not a MS9 yoke. MS9 yoke have a separate connector for the horizontal and vertical. This looks more like a MS8 yoke.
The other thing you can do is break that connector and make it into 2 connector. But I don't recommend it.
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Mark of the Wolves would be a great game to test.
And yes, I do believe it does come standard in update all, but someone with more knowledge about mister might know for sure.
The one thing I did notice about the Toshiba perfect flat in the MS9 tube is that the focus could be better. The PFX is razor sharp though. Here is my Toshiba PF chassis (PB-9929) running on a MS9 tube inside an Astro City. As you can see, it is running 31khz on KOF 2002 UM on the Y2 board.
FYI, you can also used one of the Toshiba perfect flat chassis like the 9929 on the MS9 tube. However, you'll have to make some adapters for the neck ground pin, the degauss and one of the yoke connector (I forget which one). So it's not as straight forward, but it will work.
If you have a MS9 tube, you can swap in a Sanwa PFX tri sync. Just note that this chassis is huge and won't fit on the MS9 mounting tray.
But it will work and they are fairly reliable. As for the pb7534, I could not tell you since I have never owned one.
Since you live in San Jose, you can borrow a Sega USB I/O and see if it gives you any issues. They are the same exact size and the pinouts are the same too. Plus, they have USB, so you can use it on a PC (D input only). Drop me a DM if you re interested.
That is the official Sega I/O that comes in Naomi Universal, Net City and New Net City.
When I used to have a New Net City, I actually replaced this I/O for the Sega USB I/O (type 4) and it worked great for most games. It did not like the Y2 system though (KOF 2002 Ultimate Match).