I thought it was just the inventory files which caused problems with the download version.
Unfortunately, the data.000 file contains all of the character and NPC data, as well as some quest information. It can't really be swapped between different playthroughs.
Unless you want to play at a higher and/or widescreen resolution, I'd recommend continuing with the disk version.
You can manually set the resolution to run at higher than officially supported resolutions by editing the config.div file in the main Divine Divinity install folder. The game itself should be fine, but opening the map/journal can cause a crash, the frequency of which is both system and resolution dependent (with my old computer I could bump up the resolution a notch with almost no crashing, but the problem was that it was so rare I would keep forgetting to save before opening the map, so I dropped it back down).
