The bridge and tail piece holes where out about 2.5mm as well. Plus there was no earth wire hole to the bridge. The fretboard needed a few cracks filled plus 2 frets needed gluing down. Other then that it went well.
Ouch, sounds like an uphill battle! I'm happy with my kit - it all measures up well. I've found a couple of small dings, but I have a feeling they've been made by me ;-)