Woah... I'm so glad we never had to worry about this.
I just found these pictures of a wedding:
http://square.umin.ac.jp/optical/opt...gallery11.html
And this is at the NEW Takanawa Prince Hotel (which is the lowliest of the 3 Takanawa Prince Hotels)

If people getting married at a 3* hotel are going to this kind of expense, I dread to think what they'd expect from you at the PH or MO...
My only suggestions are outside of Tokyo.
Hakone:
www.fujiyahotel.co.jp do weddings
And here:
http://www.ukai.co.jp/toriyama/ near Mount Takao (STUNNING venue!) I know they do weddings because of this photo:
http://www.ukai.co.jp/toriyama/wedding/index.htm
EDIT to add: forgot to mention that they release fireflies into the grounds in August.
The other thing to watch out for is finding an auspicious date to marry on (although you'll find better availablility and a better price if you can ignore this)
Here's a guide:
http://www1.ourtokushima.net/kankyou...y01/rokki.html
'taian' days (especially those occuring around weekends) will be booked solid.
Congratulations, anyway! And best of luck. It looks like you're going to need it....
(Are you sure you don't want to fly everyone over to somewhere like Thailand instead? I'm sure it wouldn't cost much more. Just a thought.)