Gosh, is that the same building in both pictures? Looks like someone has already done a lot of work turning the building into a home. Have you mapped out the property yet? A map and a list of goals you are working toward, that really help with planning. Gives you a visual of key features and lets you brainstorm about potential places to put things.
Old churches are wonderful structures in many ways. Often they were community built and maintained, lovingly and well. The light and acoustics inspire and welcome. Even better if there is a second-level balcony -- I always loved those. And of course, the history! The community may have faded with time; and yet I like to think the noblest part of themselves lives on.
That's a lot of space in that building, how is it going to be heated? Have you thought about any zero-emission heating options to help reduce the cost of heating? like geothermal and solar water heating for in-floor radiant heat.