Not every joystick fits every panel. Most Japanese arcade panels used an adaptor plate, to which the joystick was affixed before being attached to the panel.
You can have a look at the panels and sticks on these pages:
Used on the Super Neo 29 Candy, and probably others, this mount is the same as the ones used on Sega's Astro City panels (which were also used on many Sega cabs) except the depth is 10mm, where Sega's is 14mm. It uses only two screws, at 95mm, to affix the plate.
Several sizes of plates will fit here. The two important dimensions are 96mm for the mounting screws, and 10mm depth. You should also make sure the central hole fits your stick, but anything over 21mm should do.
Sega used the v1 panel mount for their Aero and Astro City cabinets, as well as the Sega Virtua Stick Pro. It was simple, with only two holes spaced 96mm apart, 14mm from the panel.
These three plates will accomodate Seimitsu's P=40, P=50 and Sanwa's JLF and JLX mechs, which is just about everything you'd normally expect to use.
The JLF-P-1S plate is still sold by Sanwa, but Seimitsu no longer sells any plates that fit the v1 mount.
This mount was used on the Sega cabinets that followed the New Astro City. It's much smaller than the City mount, with two 65mm screws and a 6mm depth. Seimitsu makes 3 adaptor plates to fit this mount.
The VF and SE Base plates both use countersunk screw, and will mount flush when installed. The All in One plate below does not use countersunk screws and will sit .8mm (the height of the screw head) away from the panel mount.