Bill is definitely a good resource as he knows everyone. I am happy to help with some suggestions; especially if you go to the Kansai Region (Osaka, Kyoto, Kobe, Nara, etc). Kouka-en has programs available too and you can contact Bjorn Bjorholm about the matter.http://fujikawabonsaischool.com
Aichi-en is another good place to check out in Nagoya as well as Shunka-en North of Tokyo (Yannick Kiggen is there and their display class is killer).
I'm leading a small tour in November to the Taikan-ten if the group fills up to seek Osaka, Kyoto, and potentially Nagano (Shinji Suzuki's bonsai garden). The last being mainly because I want to go
. Bjorn is has a tour website set up called The Kyoto Network. Worth everyone checking out.....
I'd be happy to help as well to recommend some sights in Tokyo. There is a marketing campaign currently going on to attract more visitors to Omiya. It's called VISIT JAPAN! and you can find them online or Facebook. Suggest contacting someone in the know before going to Omiya as I got lost often and I speak Japanese.....
If you plan your trip well you may not need a guide, but having burnt up a few days myself in 2009 wandering around, I'd suggest it.
Go for at least 2 weeks; 3 would be better. A JR or national railpass can save you a lot and open up more opportunities to travel further from your jumping off point. I think I will write something up on my blog about visiting Japan as these questions are often asked.
One final suggestion. If you think you need to save $1000 for bonsai stuff, save $3000