This is a cool topic. I don't know about houses dating back to the 1600's, but I've seen and been in a lot of older houses.
Actually, there is a World Heritage Site in Gifu/Toyama prefectures (Shirakawa and Gokayama respectively). They are houses that have basically stayed the way they were for hundreds of years.
Gokayama - Wikipedia, the free encyclopedia
Looking at the "gasshō-zukuri" link in that article brings you to another article:
Minka - Wikipedia, the free encyclopedia
That article kind of gives a run down on a lot of different styles of houses.
Machiya - Wikipedia, the free encyclopedia
(farmhouse/farmer in Japanese being searched in google images)
農家 - Google Search
Another subject that might be of interest to you is a special style of house that is called "azuma-dachi". That style of house is famous in Toyama.
As far as what I have seen inside older houses goes... it really depends on the style of house. Older houses in towns (machiya) are usually very narrow and really long (which I guess was for tax purposes?). Also, like most Japanese houses they are at least 2 stories high... so I see a lot of REALLY steep stair cases (like seriously border line ladders).
In my area there are a lot of fairly large older style houses (I don't think a lot of them are from the 1600's though... maybe 1700's and 1800's). The layout of them is usually similar. I wish I remembered the exact layout, because it is quite specific. A lot of older houses will have something called an "irori" (which is like a firepit) in them, which is used for heating up tea and doing a little bit of cooking with as well as for heating.
Another distinct characteristic of older houses that I've noticed is that they consist of a lot of small/medium sized rooms that are actually connected with sliding doors. These sliding doors can be taken out and stored (in a specially made storage rack). Doing so can open up the whole house to make almost one big room. This was traditionally used for gatherings like weddings, funerals, and other ceremonies. Something that I don't really know how to explain about the design, but I know is there is the airflow and the position of the house in respect to that. A lot of older houses are naturally cooler in the summer and warmer in the winter just by design. Of course certain rooms are better than others depending on the time of year.
As far as the wood goes... it's amazing what they used in older houses. That kind of wood simply doesn't exist any more. I think if you look up "azuma dachi" you will get an idea of what I'm talking about. If you can, try to find pictures looking up in the "irori" room. Another interesting design of those houses is that they aren't technically two floors. Again, looking at pictures is the best way to get an idea of what they look like. I've heard that when people tear down those old style houses the wood goes for a pretty penny. I think it's a waste though.
I think the information I gave you should give you a little bit of a start. Hopefully someone will have more specific information to give you. I have a feeling that a lot of the really good information on this kind of thing will be written in Japanese though, so doing a search in English might really limit you.