Good luck, having been where you are now (Link, Link), I know it can be a daunting prospect.
If you don't mind I'd like to offer a little advice.
Does the model need to have both the interior and exterior? or could it be built as 2 models, when your inside you can't see the outside and vica versa. If you build it as 2 models it will make it far more manageable.
Groups, Groups, GROUPS! I can't say this loud enough, and Layers, I'd be lost without them. Group as you go along, in the church I did, a typical column is a component(group) that consists of 4 groups (Base, Column, Capital, Details) Within the base group alone there are are 3 groups and the details group (the flowery stuff around the capital) there is probably 20-30 groups within groups.
You can always explode it later.
Beg, steal, borrow or as a last resort buy a Leica Disto, it will make the surveying MASSIVLEY easier.
Start with the floor, get this built and everything else will link to it.
Mentally break the building down in to parts - The columns -> a column -> its base, shaft, capital etc. Thais way you'll be able to put it together again later.
Photos, you just can't have enough of them. Take photos of everything from every angle.
Save things like the pews for later, this sounds a bit odd but there will be times that you'll get a bit lost in what your doing and having a 'thing' that you can start and more importantly FINISH in an hour/day/week will get you back on track.
Hope the above helps and feel free to ask away.
Edit:
One more thing.... Remember, your building a MODEL of a church, not a church itself, you don't have to get every detail right. You only have to get it right enough for it to be recognisably that column, cill, pew etc. Its very very easy to get lost in the detail.