There are photos of Bf 109s parked with the flaps in various positions from fully up to fully down, likewise the radiator flaps. Go with whatever you fancy.
As for the slats on the leading edge, it was common practice to push these in on parked aircraft to prevent an debris getting into the mechanism, potentially jamming the slats in or out. On a tail dragger, like the 109, they would stay in. I have seen pictures of parked aircraft with slats out (or even one in one out) but mostly they are in.
An important detail, usually missed by modellers is that when the flaps were wound down the ailerons drooped progressively too. With flaps up the ailerons droop 1.2 degrees which is negligible on a model but with flaps fully down (42.5 degrees) the ailerons have a significant and noticeable droop of 11 degrees.
Joe, the flaps and elevator trim were operated by the two large (30cm) wheels on the port side of the cockpit. The linkages were entirely mechanical. By rotating both wheels together it was possible to lower the flaps and simultaneously adjust trim to compensate for changes caused by the lowering of the flaps. It's a feature that British test pilots at the RAE commented positively on.
Cheers
Steve
Edit: What colour was revealed by the deployment of the slats is a bit like the Spitfire wheel well colour question. The usual answer was that the primer colour RLM 02 would be revealed, which is certainly the case in some examples. However there are plenty of others where the colour in that area is simply a continuation of the upper surface camouflage colours. Unless you have a picture of your subject showing this area your guess is as good as anybody's.
As for the colour inside the slat itself, there is colour film of some early Bf 109 Es which shows this to be the under surface colour, RLM 65. You can go with that, later RLM 76, RLM 02 primer or, on a late war aircraft, just aluminium.
......!