II./KG 1 had up to 5 Ju 88 C-6 between March and August 1942, and then again one between May and July 1943 (
http://www.ww2.dk/oob/bestand/kampf/biikg1.html).
9.(Eis)/KG 1 used up to 9 Ju 88 C-6 between January 1943 and February 1944, when it was renamed 14.(Eis)/KG 3 and lost 5 to enemy action (
http://www.ww2.dk/oob/bestand/kampf/b9kg1.html). 14.(Eis)/KG 3 transferred out the last two Ju 88 C-6 in February 1944 and then did no more use the type (
http://www.ww2.dk/oob/bestand/kampf/b14kg3.html).
Stab KG 3 had one Ju 88 C-6 between July and November 1942 (
http://www.ww2.dk/oob/bestand/kampf/bstkg3.html).
I./KG 3 had 2 Ju 88 C-6 between November 1942 and January 1943, and then up to 7 in July-August 1943 (one lost to enemy action) (
http://www.ww2.dk/oob/bestand/kampf/bikg3.html).
II./KG 3 had up to 8 Ju 88 C-6 between April and November 1942 (5 lost to enemy action) and then again 3-4 between June 1943 and January 1944 (
http://www.ww2.dk/oob/bestand/kampf/biikg3.html).
IV./KG 3 had one Ju 88C-6 between January and April 1944, probably for training purposes (
http://www.ww2.dk/oob/bestand/kampf/bivkg3.html)
I./KG 6 had up to 2 Ju 88 R-2 in September-October 1944 (
http://www.ww2.dk/oob/bestand/kampf/bikg6.html).
I./KG 6 had up to 1 Ju 88 R-2 (lost to enemy action) and 3 Ju 88 C-6 in September-October 1944 (
http://www.ww2.dk/oob/bestand/kampf/biikg6.html).
IV./KG 40 has up to 24 Ju 88 C-6 between January and September 1943, but probably for training purposes only (
http://www.ww2.dk/oob/bestand/kampf/bivkg40.html). All 24 Ju 88 C-6 left the unit in September 1943 and were transferred to another unit
II./KG 51 had up to 9 Ju 88 C-6 between March and November 1942 (
http://www.ww2.dk/oob/bestand/kampf/biikg51.html). It lost 1 to enemy action.
III./KG 51 had some in August-September 1942, and then again from March to July 1943 (
http://www.ww2.dk/oob/bestand/kampf/biiikg51.html). It lost 3 to enemy action.
IV./KG 51 had up to 9 Ju 88 C-6 between November 1943 and February 1944, probably for training purposes (
http://www.ww2.dk/oob/bestand/kampf/bivkg51.html).
Stab KG 54 had one Ju 88 C-6 (as its only aircraft) between January and March 1943 (
http://www.ww2.dk/oob/bestand/kampf/bstkg54.html).
I./KG 54 had also one Ju 88 C-6 from December 1942 to May 1943, and then up to 5 in July-August 1944 (
http://www.ww2.dk/oob/bestand/kampf/bikg54.html). 2 were lost to enemy action in 1944.
II./KG 54 has 2 Ju 88 C-6 in June-July 1942, one in January 1943 (lost to enemy action) and again one between March and June 1943 (
http://www.ww2.dk/oob/bestand/kampf/biikg54.html).
III./KG 54 had 3 Ju 88 R-2 in August and September 1944 (
http://www.ww2.dk/oob/bestand/kampf/biiikg54.html).
IV./KG 54 had most of the time in 1943 and 1944 some Ju 88 C-6, but probably only for training (
http://www.ww2.dk/oob/bestand/kampf/bivkg54.html).
Stab KG 76 had one Ju 88 C-6 between August and December 1942 (
http://www.ww2.dk/oob/bestand/kampf/bstkg76.html).
I./KG 76 has up to 2 Ju 88 C-6 between August 1942 and January 1943 (
http://www.ww2.dk/oob/bestand/kampf/bikg76.html). One was lost to enemy action.
II./KG 76 had up to 5 Ju 88 C-6 in March-April 1942 (1 lost to the enemy) and then again one between January and March 1943 (
http://www.ww2.dk/oob/bestand/kampf/biikg76.html)
III./KG 76 had up to 12 Ju 88 C-6 between May 1942 and November 1943 (9 lost to the enemy)
IV./KG 76 has 1-2 Ju 88 C-6 between March and November 1943, probably for training purposes (
http://www.ww2.dk/oob/bestand/kampf/bivkg76.html).
For some reasons I thought that all (Eis) staffeln were using Ju 88 C, but I stand corrected, the (Eis) staffeln of KG 27 and KG 55 used He 111 as the rest of their Geschwader.
From the above figures, we can see that in 1942-1943, a good part of the Ju 88 units of the Luftwaffe had a small number of Ju 88 C-6 in their inventory. Enough units for me to think that this was probably part of a general plan, but to which purpose ? Provide this units some long range escort, or some strafing punch ?
Actually I find particularly interesting the fact that KG 26, KG 30 and KG 77 are the only Ju 88 Geschwaders that never used Ju 88 C-6 according to the Flugzeugbestand und Bewegungsmeldungen reports. Anti shipping missions were a good part of the activities of these units, and my humble opinion is that it would have been a good idea to use Ju 88 C-6 as anti-Flak gunners in the same way that the RAF used Beaufighters and Mosquitoes to escort and attack escorts to protect Beauforts and Beaufighters bearing torpedoes, but it was apparently never done by the Luftwaffe (ZG 1 escorted bombers attacking convoys in the Med in 1944 but AFAIK did not strafe the escorts, being concerned only with Allied fighters).
Then in fall 1944 some bombers units again received Ju 88 C and Ju 88 R, but my guess is that it was part of the training phase to transform these units in KG (J) units rather than to use them operationally.