Prinz Eugen Info / Trivia in no particular order.
Well, Mr Eames, do you know of this thread - it is packed with links, data, and all sorts of juicy stuff. Herr Olaf Held makes many posts in it, he seems to be quite knowledgeable about Eugenish things. (And the Kriegsmarine in general.) http://www.shipmodels.info/mws_forum/viewtopic.php?f=48&t=8372
Trumpeter supplies two sets of torpedo tubes in the box, the ones with the exposed controls (F2) would be correct for the 1941 build.
The forward stabilized spherical AA rangefinders were not fitted at the time - simpler, open 4 meter rangefinders were used. Likewise, the enclosed adjacent 3 meter rangefinders at the time were of a simpler, open design. (G4)
However those same parts (G12 + G13) can be filled, sanded and modified to represent the hinged funnel searchlight cover. The kit comes with a 20 mm flakvierling in this position, which is correct for 1945 - in 1941 searchlights similar to the ones on the main-mast platform were fitted here. There was also one more of these lights on the platform forward and above the admirals bridge. (part (A11)
All the kits light and medium AA guns need to be replaced with 6 twin 37mm SK 30 mounts and 8 20mm C30 singles. Flyhawk makes nice ones.
The main rangefinder (B40) should have the ribs removed from its top. These locate the radar hut (D10) which was not there in 1941, but remove the lug for the radar mattress and the observation cupola and move them down to rangefinder. Also absent were the radar warning receivers around the rangefinder platform (G22). In a similar manner there is a two-story structure under the main-mast that needs the top section deleted. (D2 D21 D22 D27 D28)
Radar mattress and base on the main mast (A15 B19 C38 C39) were not in 1941.
A and D turrets have rooftop access ladders on the right side only - this is obvious on all photos of Hipper class cruisers - but I have yet to see any manufacturer get it right.
And finally, there are a lot of extra Marx rafts all over the 1945 version that need to be deleted. Careful study of the images on the http://prinzeugen.com/
website will give you an idea, as well as Warship Pictorial No. 21 by Steve Wiper if you can find a copy.