I don't have the equipment to align
bore/hone so I left this to Taylor
Machine in Whitter CA.   The main caps
are special high strength steel and were
made to my specs by Program
Engineering back East.  They make
main caps for many of the top NASCAR
teams.
All the mains measured within
.0003 with respect to each other
and were within .0005 of the target
nominal size.  
Another invaluable tool is the portable CMM
like the Romer Arm shown.  This measurement
tool can quickly and accurately check most all
the vital block characteristics such as cylinder
centerlines to crank angles, cylinder to cylinder
and bank to bank angles, block deck flatness
and angle to crank, trans interface to crank
angle, etc.  It's good to about .002, so you'd
still want to use individual and more precise
tools for things like cylinder bore, bearing
bores, etc, or a fixed CMM.   Newer Portable
CMMs have accuracies in the tenths, but they
cost about $40 grand.   

After my main were re-bored, everything on my
block checked out fine and good to go.  
Now that the block has been sleeved, bored, align
bored/honed, seasoned, measured and verified
the next step will be to make some mods to the
new caps and block for better oiling and then it on
to assembly.  More to come.   
The Portable CMM Arm comes in handy when trying
to determine relationships between difficult to
measure components like;
rear tire alignment wrt to front wheel wrt swing arm
pivot point wrt steering head axis wrt foot peg
position, wrt crankshaft centerline, wrt etc, etc.  
You'd be amazed at what you can discover.  Ever
wonder why one bike handles much better than a
identical model?  Manufacturing tolerances . . . .