Take the slide off and look at where the tab on the safety lever hits the sear. You can trim a little off the tab to allow the safety to engage fully, but it is just a stroke or two at a time with a file, then try it.
What has happened is that you have modified the sear and hammer enough to change the cocked rotation of the sear relative to the safety tab. Once you file down the tab enough to engage with the new sear position, it may well have too much clearance when an unmodified sear is put in the gun. Keep that in mind.
Schmeky's adjustable sear will definitely fix the problem, but getting the sear and hammer at the same time from CGW would be the safest route for you and then you would never have to mess with it again.
Having to re-do or replace the thumb safety on a 1911 after modifying the hammer and sear is common for the same reason. You can try it on your CZ safety as well. Just be sure and check it when you are done and then have someone else check it to make sure there is no sear movement when the safety is engaged and the trigger is pulled.
You can check for excessive clearance by cocking the gun, setting the safety, pulling the trigger, releasing the trigger, then observing any sear movement towards the hammer when the hammer is pulled back slightly. If the sear moves, it means it moved some when the safety was engaged and the trigger was pulled. You don't want that.
Joe