I assembled a few JST PHR-4 connectors with wires (manually crimped SPH-002T-P0.5S crimp terminals with AWG24 wires and inserted it into the PHR-4 connector housing). When I tried to join connector header with the mating PH male pin header on PCB, I find I canno to insert it there. I don't want to apply too much force to connector, to avoid PCB damage. What can be the problem there? I suspect this may be due to I created connector using manual crimp tools, and this can no provide the required accuracy. Here is datasheet.
Did you use the correct pin crimp tool, either YRS-240 or YRM-240?
These tools run around $1000 each, and are kinda tricky to use. If used correctly though, these make perfect crimps.