Regarding your 2nd query about the distinction between damaged/destroyed aircraft, the Luftwaffe was using a percentage system. Over 60% the aircraft was damaged beyond repair (or totally lost/missing for 100%) and was counted as destroyed. Under 60% it could be repaired, the place where it could be being linked to the percentage (<10% in the Staffel for example, so often not reported). 60% being the border, it seems to me it was not so clear, and my own expression is German clerks thought the same and don't use it as often as 50% and 70%, but have no number to prove it or not.
But this loss percentage is just an indication of the first report. An aircraft damaged at 50% and loaded in a train could be judged beyond repair when it arrived at the factory suppoed to repair it, while a wreck at 70%/80% could be repaired. Such cases exist in German loss lists... even if a good part are probable WNr errors.
More often, an aircraft damaged around 50%, and so requiring to be sent to a factory to be repaired, couldn't be sent there and will finish in a derelict state when the Allied overan its airfields. My guess will be that this would be the case with probably a good part of the German bombers landing or force-landing in France with heavy damage.
As for your 4th query, I think that the fact of 53 He 111s are included in the Luftflotte 3 tables seem to imply that KG 26 operations over the Med were included in it. If He 111 were not involved in Steinbock, they were used in convoy attacks up to May 1944. In
https://www.ww2.dk/oob/bestand/kampf/bikg26.html we can see that I./KG 26 lost 27 He 111 due to enemy and 5 more without enemy action between January and April 1944.
My last advice would be to cross the Luftflotte 3 with the Flugzeugbestand available on the site
https://www.ww2.dk/.