Depending on what bolts you are having problems with you can try taking pics and some of us maybe able to help you. I went through the same thing with the 1st one I rebuilt and I can say that most bolts will only fit in one place, so with some trial and error you can probably figure it out. If you are going to break down the
Engine it might be a good idea to separate the Engine bolts from all of the frame bolts. I break things down in phases now and I store the bolts for each step in an empty 2-liter bottle with the top cut off,so I end up with one for yz top end and such .. I am not aware of any kit that says 'put bolt A here', but you can look at a parts microfiche on a site like servicehonda.com and see what mm bolt is being used in any given location. the service manual may list some of the sizes as well.