If I remember well, the changes to adapt it for 1.0005 was a few lines in task_manager.script and xr_motivator (I don't remember well what was changed on those since the last time I did that was a month or two or three ago) and also system.ltx (change the current_server_entity_version from 6 to 7).
For example, check this compatibility thing I've upload for O.F.F.L.I.F.E. mod.
My thoughts for xr_motivator, the changes were related to the dialog_manager lines script.
One thing I've found rather frustrating is that a lot of the really cool Russian mods out there are built with 1.0004 in mind. I remember that the original AMK mod was done with this in mind aswell, and there was a patch you could use to make the 1.0004 version into 1.0005 (I use the steam version, so this is pretty much the only version I can use)
Is there some sort of universal method to adapt 1.0004 to the 1.0005 patch? I know some stuff was changed in the patches, but I'm unsure as to what it is. Any thing to look out for in terms of pitfalls and what have you would be great.