This has been posted for sure...hasn't it? Well, here it is (again, maybe).
http://justkdx.dirtrider.net
CDave's site is a place you MUST read through. Jetting advice for all the mods you mention. Starting places, for sure! Your particular bike MUST be jetted to suit YOUR particular bike...and you, too!
The boyesen reeds come with their own 'stops'. You do NOT use the oem stops. BTW, the oem stops are heavy large metal 'tongues' that are only about 45º from the reed. The boyesen stops are little metal strips that amount to acting like not much more than a washer under the screws. This said cuz someone may have removed the oem stops from the oem reeds thinking they were hotrodding something.
re: removing the bearings.
If you remove 'em, replace 'em. No reason TO remove them, though. You can clean them and regrease them with them still in the part. If you don't have a lower mount shock bearing on hand, be prepared to let your bike sit while you wait for the one you order. I'll bet'cha it's toast!
No 'special tools' needed.
Pay close attention to the re-assy of the rear linkage assy. The bolt shoulders are a bit short and it's easy to tighten the pull rods AGAINST the shoulder instead of having the shoulder placed THROUGH the rod. This is particularly easy after you grease the assy, cuz the seals are full of grease making the bolts effectively even SHORTER!
You should be able to lever the rear on the kickstand...touch/bounce it some on the ground. There should be NO movement that's not activating the shock spring. NO free play whatsoever, nowhere.
Oh...set your race sag first thing. Well...kinda gotta after a spring replacement. Seems a commonly overlooked item...and about the most important suspension setting you can/should/have to do.
But hey!! ....Every FOG knows about that, I 'spose. ;)
Have a blast!!!
***edit***
BTW..use the best grease you can get. A waterproof marine application grease from belray has been used to good end by some posters. Your general one each moly chassis lube won't work. Well...won't work meaning you'll be replacing the bottom shock bearing OFTEN if you use it. I went through about four of 'em (replaced with sleeve and new seals at the same time) before I got some good grease (hydrotech parasyn70).
Brakeclean is a good product for cleaning the bearings. Makes a mess! But it works!! (eye protection a good idea)