Crankcase
The crankcase thru bolts or captured studs, as the case may be, should be tightened a little at a time. Take care to keep the case halves as even as possible. I use some heavy aluminum plates under the thru studs to better distribute the loads and avoid scoring the area where the cylinders mount.
The way I interpret the manual is that all these thru bolts/studs should be torqued while assembling the case halves. When the cylinders are installed, remove the hardware for that particular cylinder, install the cylinder and re torque.
In my opinion removing the nuts just before installing the cylinder keeps the bearings seated better.
Lycoming only has a sequence for a few of the perimeter bolts. (1/4" bolts around the case perimeter)