Assuming you have the swingarm, linkage and shock off for a normal service, this is what I do:
1) Assemble linkage on bench, with main rocker/bracket bolt hand tight. Pull rods on rocker hand tight.
2) Install linkage assy in frame, install swingarm pivot shaft temorarily to locate brackets relative to frame and engine cases.
3) Torque bracket to frame bolts, main rocker bolt
4) Install shock, bolts hand tight
5) Remove swingarm pivot, install swingarm, reinstall swinarm pivot hand tight.
6) Loosen engine mounts and head stay
7) Torque swingarm pivot 81Nm
8) Torque engine mounts, head stay
9) Temporarily install pull rods to swingarm with bolt, without nut
10) Raise swingarm to preload suspension and take out shock mount play, snug lower shock bolt with open end wrench, torque upper shock mount.
11) Remove pull rod/swingarm bolt and swing down pull rods, torque lower shock bolt.
12) Re-install pull rod to swingarm bolt, again preload suspension, torque pull rod bolts 81Nm.
Note:
Using the swingarm pivot temporarily as a locator when mounting the linkage brackets makes mounting the swingarm much easier, as the holes are pre-alighned and cannot be pushed out of place.
If your frame is such that the linkage brackets are a real PIA to R&R, you can loosen the motor mounts before installing the linkage to the frame. After its in with the pivot temporarily installed, snug them back up so they do not fall out of place when the pivot is removed again.
Sounds like a lot of work, but it took longer to type than it does to do. Been doing it this way since '00 witn no problems.