@Marcel, I generally agree with your thoughts regarding the wings. But just to be clear, I'll start from the top
Why would there be revisions? There are TWO major reasons that this would be the case; the first would be correcting structural weaknesses or suspected points of concern that have arisen during the operational testing and initial deployment of the a/c, while the second is (as you rightly point out) the need to include upgraded components.
To look at the second point, the desire to fit the Jumo 213 and 222 engines came about after the initial design was completed, so its quite logical to expect that the 512 wing in particular, featured changes in order to cope with the forces involved from (at least) the Jumo 213E and the more powerful DB603's - I suspect the Jumo222 would have required another redesign again due to the very different shape and weight distributions.
Another factor that may have brought about a change in wing designation, would have been the shift to a single conductor wiring layout and possibly the change in fuel system (which would have required modifying the 501 and 506 wings in order to retrofit the A-7 fuel system). BUT hopefully its not something as subtle as thing; hopefully it is a structural change!
Now to the first point - all manner of forces act upon an a/c that can go unnoticed or unappreciated for a considerable time - the best example I can think of off the top of my head (again) relates to the FA-18 fleet. The a/c very early in there career's were fitted with fin reinforcements and a small Vortex generating blade on the LERX in order to stiffen the fin and change the vorticies striking the upper parts of the fin in high energy/high alpha flight. These changes were subsequently incorporated into the basic design.
It is more than likely the He 219 also experienced such design changes - and for the sake of IDENTIFICATION, I hope i) the changes are structural (and not just wiring or something small) and ii) the changes were not retrofitted to the fleet. If the changes were retrofitted to the fleet, that will suck
As for parts of the a/c that remained the same, that makes sense as well - as they say, "if it ain't broke, don't fix it!". I can see this being true for the engine covers, access doors, whatever.
As for the He 219 engine bearer design, its quite elegant actually, how parts of the load bearing members essentially form the aerodynamic structure and skin, YET still is a quick release 'power egg' type design. Not only does it save weight, but also saves complexity.
Good luck with examining the wing drawings BTW