gunman_: From the unofficial patch 1.005 you can use only the executable (and osiris.dll), it appears to be working over the gog version (played a little) but I don't know if it will break something else later.
In terms of know issues, there is very little difference between the 1.005 and 1.006 versions; Larian had to re-do the higher resolution and widescreen support due to a problem with the updated source code accidentally not being included in the working backup they had, and other backups not being readable. IIRC scorpion traps were nerfed in 1.005 and back to overpowered in 1.006, there were a couple of other very minor differences.
The only significant (IMO) exception is that there was a
music fix for the 1.006 release of the game, which will not work with the 1.005 version.
It would be interesting to play around with some of the updated files from the original 1.004 download release of the game, but there was also a critical game breaking bug in that version (the screwup with reverting some of the source code happened when fixing that bug), so there might not be an easy way 'patch' the lost changes back into the current release.