I have the minimalist set in the front room, modern and half of sleek set in the back room, astro set in the right side room, and classic in the top floor. The left side room has a few trendy pieces but mostly kitchen items. I've also been using moridb heavily to check whether an item matches the theme.
@Nao - I DID NOT order the golden door. I do not have any of the golden exterior items and I didn't change any exterior elements.
Sorry - I would guess you did not, but the wording wasn't absolutely definite as to whether you did or not, so to be on the safe side...
Anyway - I'm no expert on the theme challenge, but I'd really recommend putting all of your themed items within ~3 rooms rather than spreading them out. If you don't have enough items in a room so that it makes 90% of the room and is at least ~10 or so items, then it'd be best stuffed in a room that already has a lot of those items. Non-themed rooms don't count against you, but themed items in a predominantly non-themed room aren't making you a lot of (or possibly any) points. Your "mostly kitchen items" room would probably be most useful if you took the trendy items out of it and put them in a themed room.
Again, I'm no expert and I'm not trying to tell you what to do. >_< But I completed the challenge in a couple of days with three rooms absolutely stuffed full of sci-fi stuff, so in my experience, I think stuffing a few rooms is your best bet.
Taken from Liquefy's FAQ on gamefaqs, the formula for a house with at least 3 exterior reforms and 90% of items in a room being themed:
90% of room for 11,000 x # of total different items + 95,000 x # of exterior reforms
You've probably seen this before, but in case you haven't, here it is.
EDIT - also just in case, here's a link to that FAQ.
http://www.gamefaqs.com/3ds/997811-animal-crossing-new-leaf/faqs/65246 This is what I used, it has all of the themed items in one easy place.
But yeah, I definitely can't explain why your score would drop.