Okay I have some info here for you since looking it back up in my book.
Ju-290s
The Ju-290s not the Ju-390s were actually used to fly to Spain and only 2 were known to actually have flown there. The first one was Ju-290A-3 W.Nr. 0161, Identification code: 9V+DK and it crashed in Spain on Dec. 26, 1943.
The other was Ju-290A-5 with Civilian Lufthansa markings D-AITR. It was flown to Spain on April 6, 1945 by Flugkapitaen Suzalek. There was a manifest for this flight that included Hitler, Himmler, there families and several other high ranking Nazi officials. None got on the plane and it is believed to have carried valuables for safe keeping.
This Ju-290 overshot the runway in heavy fog and ended in a rice field with very little damage. It remained there until it was sold to the Spanish Airforce on April 29, 1950.
There 13 Ju-290's in service with KG200 (I can give you W. Numbers if you wish and Ident numbers) Of these thirteen Ju-290s, 2 crahed in Spain as told above, 1 was bombed and destroyed in Tours on Feb. 5, 1944, 1 went missing in action on the Russian Front on June 16, 1944, 1 was destroyed on the ground at Dessau on Aug. 16, 1944, 2 were destroyed on the Eastern Front on 11 June 1944 and 23 May 1944 respectivly.
Of the 6 that survived the war (not including the one that crashed in Spain and was later used by Spain) one was sent to England with the markings of AM 6 on May 5, 1945.
Ju-390's
There were 2 known Ju-390s used by the KG200. There is very little information on them though. Ju-390V-2 just being noted in Oblt Joachim Eisermanns logbook. According to his logbook he flew the Ju-390V-2 at Rechlin in February 1945. There is no known W.Nr. on it though and no identification numbers.
The other Ju-390 was a Ju-390V-1 with tail identification markings of GH+UK. It was not used very much and was destroyed at Dessau in 1945. I have a picture of it in my KG200 book in Prague-Ruzyne sometime in the winter of 1944-1945.
If anyone would like to read up on this and other KG200 aircraft and operations the books is:
KG 200 The Luftwaffe's Most Secret Unit by Geoffrey J. Thomas and Barry Ketley