I just got Xuanlong Assault Rifle and installed Laser Sight and Extended Capacity using WMK, but now my Pipboy says its damage is 125?! WTF?!

The damage display for weapon stats are flaky in FO3 to begin with. Use the Weapon Scanner mod (the stand alone version or one bundled with FWE) to see the actual weapon stats instead.

I added a silencer, laser sight, extended clip, and a scope to my 10 mm sub. now the damage is over 100. I am thinking it is par for the course. If I were you, I wouldn't worry about it.
maybe take it to Point Lookout and see how much higher you can get the damage rating. :gun:

EDIT: must...type...faster.