In search of a little advice

In November My family and I (A party of 5) Will be taking a trip to Japan. It is our intention to get an overall feel of Japan. We will be following the 6 Night Itinerary provided by this sight(http://www.japan-guide.com/e/e2400_tokyo_5.html) as a guide to our trip. But rather than spend two nights in Kyoto it is our intention to spend a night on mt Koya. Now I have been trying to work out an Itinerary for each day and using this page as a guide.
(http://www.japaneselifestyle.com.au/tokyo/tokyo_itinerary.ht...) I am trying to plan our day in Tokyo. My wife has been getting on my case about planing this trip but to be frank I find it Quite intimidating and Ive been "scared" into inaction. But NO MORE! My questions are as follows.

1: After having looked over these guides quickly does our trip look plausible. Specifically the 1night in Kyoto to one night on mount Koya?

2: Where should I stay in Tokyo to ease travel from it to our destinations as described in the one day Itinerary. Also if you choose to be so specific as to recommend a hotel (or whatever it may be) keep in mind that the cheaper the better! Were not exactly picky people.

Any help will be more than appreciated.

Thank you,
Drew

To be honest, I don't reccommend interregional travel with 6 days in Japan, unless you wont visit it forever again.

Japan has 2 major on-the-beaten tourist destinations, urban Kanto(Greater Tokyo) and historic Kansai(Greater Osaka/Kyoto). With really short stay in Japan, you SHOULD give up one to make the most of your time(& money) in case it's possible for you to visit Japan again.

It would be probably be better to spend the time based in Kansai- perhaps visiting Osaka to get the big city feeling of Tokyo. If you did definitely want to include Tokyo, then at least 2 full days would give you a chance to experience more without rushing from one place to the next. Are you flying in from Tokyo?

My first advise is to skip mt Koya, because it takes quite some time to get from Kyoto to mt Koya (about 4 hours), from Osaka to mt Koya isn't covered by the JR-railpass and mt Koya is a big place, too big to see on a afternoon or morning. Besides this, Kyoto has so much to offer and for first-time-to-Japan very easy to get around.
About hotel in Tokyo, it's best to find one near a JR station, so you don't loose too much time and most popular sightseeing spots in Tokyo are located near JR stations. My favorite is the Shinagawa Prince hotel

While I would love to have another go at Japan after this im afraid that I dont see it happening any time in the foreseeable future. My wife and I will be trying to have a kid, and after we get comfortable again we will be going on her dream vacation.

Although I understand why It would be advisable to limit my stops it really is my intention to make this a whirlwind trip cramming in as much as humanly possible. Also I really am stuck on the idea of visiting mt Koya and staying at one of the Temples. I just gotta do it despite the set backs.

Thank you much for the replys so far.

Don't worry about me folks Ill be able to take it ^^ Im a seasoned traveler.

Hi Drew,
It looks to me that if you really want to see Mt Koya, then I would suggest not returning to Tokyo. You are losing a lot of time travelling back where you came from. If you could arrange a flight home from KIX it would give you more time in Kansai area and you could re-arrange your itinerary accordingly. t :)

Maybe it's an idea to take the nightbus from Tokyo to Kyoto (and v.v) They depart around 10PM and arrive around 6:30AM. This will save you a lot of time.

Bert suggested the Prince at Shinagawa but Drew asked for cheaper so I suggest the Toyoko Inn which is right across the road from the station and considerably cheaper than the Prince. Oh, and it is modern, clean and comfortable. Just doesn't have bells and whistles.