This a government website that breaks the trail section by section. You can navigate it by clicking the pictures of the section you want to see. It is one of the more comprehensive sites I have found. There are no topographical or GPS maps on this site. This site also has other hiking trails in Japan
This the offical website of the trail. It breaks the trail section by prefecture. Once you go to the prefecture you can find information on the particular spots. It is a decent site, but there are no topographical maps or GPS maps on this site.
This a blog from a man who hiked the Tokai Nature Trail over the course of several years. The blog was last updated in 2007, so it might be a bit outdated but it breaks things down so well. There is also bus schedule information, which may be outdated. It does give you an idea of how frequently buses run however, and where they are located on the trail.
As of 2/19/19 this site seems to be down. I am leaving the link for now, as I hope it comes back up. It is one of the best Japanese resources I have found.
I purchased the three trail books about the Tokai nature trail from Amazon.jp. They are all in Japanese, and have basic maps. I think they were worth the purchase. I have also upload the maps from the books with some English annotations. Even if you don't speak Japanese I think they may still be worth it. They were published in 2000. The books overview the trail and are broken up into three sections.
東海自然歩道30選 関東編―東京・神奈川・山梨・静岡(Tokai Nature Trail 30 Selection Kanto Area - Tokyo · Kanagawa · Yamanashi · Shizuoka)
東海自然歩道31選 東海編―愛知・岐阜・三重 (Tokai Nature Trail 31 Selection Tokai Area - Aichi, Gifu, Mie)
東海自然歩道30選 関西編―大阪・京都・滋賀・奈良・三重 (Tokai Nature Trail 30 Kansai Area Osaka, Kyoto, Shiga, Nara, Mie)