This is what I do, other opinions may vary:
Install the linkage including pull rods to the frame with the bolts loose. Temporarily install the swingarm pivot to align the linkage brackets/frame/motor. Tighten the bracket to frame bolts and main rocker bolt. Install the shock, put some upward force on the lower mount to take up play and torque bolts. Remove the swingarm pivot and reinstall with the swingarm. Install pull rod bolts and torque everything with a load on the system (bike off stand).
I found the key is getting the linkage aligned first before the swingarm. Also, some bikes are just a tighter fit than others and loosening the motor mounts helps, as does a rubber mallet.
