When you say that it no longer runs true, does it have lateral movement, or is it no longer concentric with the axle?
Lateral runout could be due to burrs on the edges of the enlarged holes in the disc which are preventing the disc from sitting flat against the machined face.
If this is what's causing your disc to run out of true, it should be simple to fix by simply removing any unwanted burrs to allow the disc to seat correctly against the disc mount/cooling fan unit.
The centre of the disc usually locates over the raised lip in the centre of the disc mount/cooling fan assembly to ensure it is reasonably concentric with the axle:
If any of your drilled holes are so offset that they are preventing the disc from locating over this lip, then the holes may need to be filed slightly with a suitable round file to allow the disc to remain centred correctly whilst also allowing the retaining bolts to thread in easily without binding.
However, if the problem is due to a buckled disc, bicycle discs are thin enough that they can usually be trued to an acceptable level with the aid of some gentle persuasion from a wooden or rubber mallet to carefully reduce any high spots.
If you don't possess a wooden or rubber mallet, a metal hammer using a block of wood between the hammer and the disc to prevent damage to the disc surface can be used instead.
I find it is best to do this while the wheel is fitted to the bike so that you can use the rubbing sound of the outer disc pad
(or a marker pen held against the caliper) to determine exactly where the individual high spots are on the surface of the disc.
Alan
