This is what I have discovered and applied so far - still quite a few to draw yet though:
Version list:
Ju-88 A-1 Standard first production model
Ju-88 A-4 (Early) Long wings and improved engines. Exhausts are changed from the A-1, and there are bulges in the cowling below the engines.
Ju-88 A-4 (Late) As above, but also the rudder is changed, and the canopy has a raised back and twin guns facing the rear.
Ju-88 A-5 Same as A-1, but with the longer wings of the A-4.
Ju-88 A-14 Special ground-attack version of the late A-4 with fixed 20mm cannon in the nose.
Ju-88 C-4 Fighter based on the A-1 but with a solid nose and different lower gondola, also the rudder is the same as the late A-4. Short exhaust shrouds on night-fighters.
Ju-88 C-6 Fighter based on the late A-4 including raised canopy, different aerial arrays, solid nose, with various radar setups. Schrage Musik gun or guns in top of fuselage, long exhaust shrouds on night-fighters.