I personally have not had any malfunctions using a rail mounted light. Though I seldom use the rail mounted light. It had limited utility unless you have a holster that accommodates the gun/light combo.
I recommend 300-400 rounds to shakedown a new gun. That's about when you can say its broken in.
If you have custom parts set, that's great. I will suggest that there are vendors like Glock who make a stock gun that's ready to go out of the box.