had a similar issue.  first check to ensure a good spark.  throw in a new plug to be sure and get the plug grease to ensure a good fit with the boot and no arc’ing.  Then if that’s ok, go to the fuel system.  Mine started running again after rebuilding both fuel pumps, and replacing the pulse lines.  empty these after every race.  Also, if someone accidentally used the wrong oil, or a low oil-fuel ratio, it can cause problems.   if all else fails, check stator in case it was knocked out of synch.  also check all ignition connectors.

Non-starts can be caused by:

Low compression, or fuel or ignition problems.

We had a non-start issue once which was caused by a failed ground strap.  The wire was coated, so we could not see that it was broken internally.  New ground installed, started instantly.

You need fuel, spark, and compression. Check the compression and make sure you do not have a broken reed. Even if you have someone pull it in sixth gear and put your thumb over the spark plug hole. Be sure to ground the plug. Next check for spark. Pretty hard to see on a CR125. Ground the plug and cup your hands over it while someone spins the rear wheels. If you have that, then the box, stator, coil, and grounds are good. The last is fuel. Is the plug wet or dry? If its really wet, you also may have the bottom of the crankcase full of fuel. Ground the plug and spin the motor with a strap off of the wheels with the plug out. If you are flooded below, you should see a mist coming out of the plug hole. If so, put in a dry plug either new, or known good and let it go. You can also try turning it over on a start with the accelerator all the way down. If it catches, be sure to let up. CR125’s are really reliable and should not be hard to start. Check out some of these items and report back.

Be sure to clean out the pulse line. When you look at the other pump, check the pulse side for being full of fuel.

No. Fuel accumulates in it and part of regular maintenance is to wash\blow it out. I don’t know where your pump is located, but check the line for cleanliness. This is the one that goes from the nipple on the side of the reed cage to the port on the pump. This sends the pulse to the diaphram in the pump to pull\push fuel. Check for a nice short routing of the line and usually you want the pump higher so fuel can drain back. Keeping it clean will make fuel delivery more efficient. Also make sure there is no kinks in it and that you are using a fairly thick walled type of tubing.  Some people use the one with the braid in it, or Motion-Pro which has a super thick wall to prevent kinking.