I think most patches are already installed and not need to be activated with Jsgme. Just adjust the option selector.
I can't say only about the chronometer at the moment, i haven't gotten there
For example:
https://postimg.cc/DWB0wQ36
https://postimg.cc/k6H5xn4t
https://postimg.cc/bDrJDGzh
I recommend starting the game through the Sh3commander
Some time ago the game crashed while watching a Victory ship from the Sh5 ships. I decided it was due to my weak computer , now i haven't tried it yet