I believe all E model 109 were built before the change in cockpit colour, so the cockpit would have been painted RLM 02, as would the weel wells, landing gear legs and inside the gear doors. The weels were painted gloss black.
The tamiya Messerschmitt is a very nice kit, although I haven't built one, I've seen plenty of reviews and comments about this model. Should be a joy to build.
I have built the Hasegawa Bf 109 E7 Trop, I'll post a couple of pics, soon.
Mal