Carpenter, Ship builder, now Stone Mason... is there no end to your disguises?
A nice idea, not many Churches are used in dioramas, but they are some of the best backgrounds, or indeed centrepieces, for an impressive diorama.
First off, my following observations are for North Western European, classical churches. If you are planning a more modern church, or a different area ( Southern Europe, the Mediteranian for example) then please ignore my ramblings..
I know that these are just the first steps, but I think it's best to throw in one observation right at the start. I think that the windows are to low. Most, if not all churches that I know have the windows start at least at some six feet above floor level. Also, and I see that you have already started this is some way, many churches are a hotch-potch of original building, with many additions, extensions, and alterations. Very rearly are churches trully simmetrical. This goes for windows as well, as often windows would have been donated (as in sponsored, paid for) by wealthy local people. (primarily to show off, and to buy a proverbial 'stairway to heaven'..) In such cases the room for such windows would have simply have been made were it was convinient, without much thought for architecture. Likewise, the very rich would add private chapels or crypts, which would be added with the stone, and architecture of the period. Considring that these churches where 'developed over centuries, the veriety of styles can be huge.
Cheers
Henk