Wow... that's quite impressive. Mine is just a 'stick drawing' (all lines) but you have definitely developed it quite nicely.

As for the upstairs you're quite right I should shorten 'long' pew and shift both down 1 square. But as the place is an abandoned chapel its not overly important as my would be heroes are going to move things about a bit.

Only place I'd change yours is the steps leading to the pulpit, as the pulpit (to me) should be centered towards bottom right corner and generally square up the pulpit area. It actually has a secret stair case leading down (shhh don't tell my players!) to an area which was previously where the church kept important records and such.