While this site is focused on travel, these questions do seem to come up frequently enough that maybe there should be a group for it!
Implementation of services is done by the city/town/ward, so the best thing is to look at the website of the local government as they tend to have English versions of their sites, or offer machine translation.
The basis of all services, though, is the 障害者手帳 (shogaisha tech, or disability ID). You get it through your local government, but it is from the prefecture and recognized in other prefectures. You do need this for getting discounts etc, or applying for disability pension. The disability pension does require the ID, but having the ID does not guarantee getting a pension, etc since that is a function of current and past income. Basically the ID just let’s people, organizations, other governments know that you have been certified as having a disability.
As for guides… I’m not sure I know of any other than the suggested local government sites. If you live in a bigger city, the city hall may have interpreters on hand to help you when applying…