I don't think an egr valve could do that.
My 99 sc2 smoked real bad befor I got it when I opened it up I found a lot of the same things as what is being described here turns out the cylinders where honed out so far the rings would not seat. Also had a bent valve on the exhaust side I didn't know about.

 

In this case, I don't think the bore is in question since all the cylinders were in spec in a compression test. That would suck to get an engine machined only to find out they screwed you out of a set of pistons and rings.

 

Mine was only 4 thou out but that was befor I got it. So I didn't get screwed out of piston and rings

 

Ah, that's a good thing.