The pistons are slightly different. The compression ratio change isn't much. On the 98 and early 99 it goes from 9.8:1 to 10.0:1. On the late 99 and 00 it's more, from 9.8:1 to 10.25:1. The rise was to help compensate for the slightly smaller bore on the later engines.
Under the circumstances of getting a low mile replacement engine for such an exceptional price, I would be inclined to suggest that you swap the SVT pieces from the old engine over and call it close enough. You will end up with most of the horsepower that you had before but have a fresh engine. If you hold out for an SVT engine, you may end up with an engine in much poorer condition.
