15 day Japan...advice needed

My boyfriend and I are going to Japan for 2 weeks and we were thinking of visiting tokyo, nagoya, kyoto and osaka. Arriving and departing on a Tuesday from Narita Airport. We will be spending the first 6 nights in Nagoya since my boyfriend has friends there. (We made the mistake of booking both flights to tokyo, so we have to get on nagoya on the first day...=/)

Here's a rough breakdown:

Day1) Tokyo-Nagoya
Day2-6) Nagoya
Day7) Nagoya-Kyoto
Day8) Kyoto-Osaka
Day9) Osaka-Tokyo
Day10-15) Tokyo

Should we get a JR pass for 7 days? If we do, when should we use it?

We havn't booked any accommedations yet but...do ryokan take walk-ins? Would the price be higher than if we had booked online? We'd like to experience a ryokan for one or two nights, but unsure of which city to book them in. We were thinking of probably staying at one in kyoto/osaka..does anyone have recommendations for ones there?

I heard that certain areas in Tokyo are better to go on certain days of the week...some recommendations would be most welcome!

Thank you very much~! We are a little scared but very excited!

Your schedule seems fine. And a JR pass would be a good idea. Use it anytime you need the train.
Now on ryokans, since they're so small you'll be lucky to get a successful walk-in. Find one in an area that you will be staying in and make an early reservation. It's a good idea to make this reservation a few months before leaving just to make sure. Hopefully, you won't be traveling to Kyoto during the fall when the leaves are turning because that's a crowded season.
To find a ryokan, use japan-guide's hotel search at the home page to the left. Under hostels and ryokans, you'll find something. If not, do a google search.

Should we get a JR pass for 7 days? If we do, when should we use it?

Regular tickets are likely to come cheaper than a 7-day or 14-day Japan Rail Pass.

We havn't booked any accommedations yet but...do ryokan take walk-ins?

It is very unusual. I recommend to give an advance call for your and the ryokan's convenience.

We'd like to experience a ryokan for one or two nights, but unsure of which city to book them in.

Kyoto has some of Japan's finest ryokan. The price range is considerable. If you have a big budget, I recommend the Tawaraya.

I heard that certain areas in Tokyo are better to go on certain days of the week...some recommendations would be most welcome!

Harajuku on Sundays. Disney Resort and the Ghibli Museum on weekdays outside of the school holidays. Museums and Tsukiji Market not on closure days.

Thank you guys for your replies. We were looking at the ryokans in kyoto...and while they look really nice they are too out of the budget for us. We are looking for something around $100 per person per night...if anyone has recommendations for ones in kyoto..or anywhere in the cities we will be visiting...please let us know. Thanks.

This is a little off topic but...my allergies have been bad during fall up here in Canada, should I bring some allergy pills for my trip?