I did a comparison in Virtual Dub of the 3 versions I have, my Z2 retail, a Z1 rip I found, your V2 restore.

I took a scene every 10000 frames and looked what the actual start frame was on each version

	DVD Z2 Retail	V2 restored mkv	DVD Z1 avi rip	diff V2-DVDZ2	diff DVDZ1-DVDZ2
horse	905	902	897	-3	-8
stairs	11270	11267	11262	-3	-8
orchestra	20516	20514	20508	-2	-8
stanzi	29585	29581	29577	-4	-8
salieri piano	40330	40323	40322	-7	-8
moz paino	50548	50539	50540	-9	-8
dancers	60062	60049	60054	-13	-8
priest	70064	70048	70056	-16	-8
salieri teardrops	79987	79945	79979	-42	-8
laughing	90208	90138	90200	-70	-8
girl	99973	99900	99965	-73	-8
discussion	109899	109824	109891	-75	-8
back	119965	119888	119957	-77	-8
crying	129916	129839	129908	-77	-8
door	139349	139272	139341	-77	-8
walking snow	150129	150049	150289	-80	160
singing	160069	159989	160229	-80	160
maid	170667	170587	170827	-80	160
walk snow	180116	180037	180276	-79	160
bed	189976	189894	190136	-82	160
writing	200111	200028	200271	-83	160
stanzi	209308	209223	209468	-85	160
priest	219893	219808	220053	-85	160

So you see the Z1 and Z2 version are in sync ( there is a 168 frames jump at a moment but I checked and the Z1 has a 168 frame black scene).

But your version slowly drifts from -3 (initial offset) to -85.This can't be corrected by just editing 2 scenes, and unfortunately will prevent adding foreign language tracks and subtitle tracks to your version to built the ultimate "all version" like the Harmy Star Wars edit.

Still, I aknowledge the hard work it must have been to edit the movie scene by scene, and perfectly understand if you want to keep it as it is. Even if it means I'll have to continue watching my awful PAL DVD ;-)

Thanks!