Christ....let's reinvent the wheel.
Align honing is done with a long mandrel. It goes through all the mains at once. Align boring is done with a tool bit. It does one main at a time. Generally align boring is done when caps are replaced. Generally align honing is done to correct diameters, straighten, when studs are installed, etc.
Align honing... the caps are cut about .005". (machinist preferences here). Align boring, caps need to be cut more than that.
Align honing... let's say you cut your caps .005". Let's assume you had minimal issues... this will move the mains up .0025 (based on average material removal). If anyone on here running a damn boat thinks this makes 2 hoots in hell regarding their mains to cylinder relationship, they are fools. Hell, 1/2 of the shops out there cannot get the cylinders to .002 round and straight. Hacks!
Align hone/ bore/ deck/ assemble.
It is not rocket science.
Wags
Oh, and BTW, sunnen recommends if a cap is getting bigger than the others, that cap is removed and recut. This will help the mandrel to straighten up. Loosening the cap every time magnifies the issue.