I am planning a holiday 8 Sept - 19 Oct 2017 Starting at Wakkanai and finishing in Fukuoka then8 days in Tokyo would a JP rail pass be the best way to see the real Japan and the 4 main Islands. I don't want to use the the bullet trains unless I really have to This is why I was looking at a one way car rental Wakkanai to Fukuoka then fly to Tokyo for the 8 days
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Renting a car only makes sense to see an isolated area that is not served well or at all by public transportation. Toll charges for Japan's highways are very high as is the price of fuel (varies, but about US$5 a gallon). Not to mention drop off charges for leaving a car at a different location than where you rented it are very stiff - the further the distance, the more expensive it is. The cost of taking a car from the tip of Hokkaido and leaving it in Kyushu would be exceptionally high.
Your notion of not taking the bullet trains also makes little sense - they are fast, safe, and extremely punctual. With the right rail pass and enough travel it is also quite economical.
Given the long length of your planned travel, your pace will likely be fairly slow and so a series of regional passes will likely serve you better. You could use some rental cars around a local area when it is more convenient. Hokkaido is a prime example of this. You could rent a car is one area, see several local sights, and then take the train to another city and repeat.
From Sapporo down to near Tokyo, there are also several flex passes that you can use - they allow a long time to see a lot of areas over 14 days, so you don't need to rush. Combined with out of pocket travel for short distances, they are a great way to see a huge portion of the country. Three of them are the JR East South Hokkaido Pass, JR East Tohoku Area Pass, and JR East Nagano Niigata Area Pass.
I suggest you look at those as well as others, all are explained in detail on:
http://www.japan-guide.com/e/e2357.html
There are some good previews of the places you may plan to see on:
https://www.youtube.com/user/thejapanfaq/videos