HI Dan, pretty sure all the tolerances will be different, no one is that lucky..! If you can't find the exact model manual then just Google it and see if anything out there matches your needs, sometimes you can find separate pages rather than the whole thing on the net. Someone somewhere will have posted about your bike and they will have had the same problem.
Found this https://www.ebay.co.uk/itm/YAMAHA-MOTORBIKE-PARTS-LIST-MANUAL-XJ400S-4BP1-JAPANESE-E837012-1-114BP-010J1/152872491691?epid=629461846&hash=item2397e91aab:g:yLoAAOSwTuJYxW6Q on ebay but at £27 a bit steep and it's a parts manual not a service manual.
Also found this one BUT it's in Italian so your gunna have to translate it using Google translate, but better than nothing https://www.ebay.co.uk/itm/NEW-YAMAHA-1986-SERVICE-MANUAL-XJ400-500-550/351476248151?hash=item51d59dee57:g:A5MAAOSwN2VZUSBx again it's £35 so not a cheap option.
So right after you read this your gunna hopefully do 2 things, one is say "Hello" in the new members section (folks like to know your not a one hit info only wonder) and second look at the adverts I put up, but if I can find those in 3 minutes you might find one even better in time.