Is the CP cost of an AG movement one CP for each additional army comtained within the AG? Therefore, would Napoleon leading an AG with Davout and Ney cost three CP's per duchy?
You are correct, it costs an extra CP for each additional army per duchy.
Furthermore, does it cost more to enter an unflagged duchy with an AG? Would it then cost the Napoleon AG four CP's to move into an unflagged duchy in Russia?
It depends on the situation. Normally it does not cost more for an AG to enter an unflagged duchy. However, if the AG contains an Imperial Allied army (Prussia or Austria) then it may cost more to enter the duchy (see section 10.12). Imperial Allied Armies will generally move to duchies that are under their control (with some card event exceptions). If the duchy is not under their control then an extra CP must be spent for them to move into it. The way around this is that armies can flag adjacent duchies as long as no enemy army can intercept or no enemy formation is present. French leaders can flag for France or their respective Ally. For example: An AG with Nappy and Yorck is moving. Nappy can flag the adjacent duchy Prussian for 1 CP (assuming no chance of interception), then move the entire AG into that duchy for 2 CPs and repeat this process until he comes to a duchy with a Tsarist formation or a duchy which a Tsarist army can intercept into. Then the AG would need to spend 3 CPs to move into that duchy.