How can I ensure precise alignment of wooden parts assembled with bolts?
Specialty Bolts


Some bolts have long smooth shanks and short threaded sections.  If you are able to find appropriately sized bolts like these, and able to buy a drill bit that is the same diameter as the shank for a sung fit, then this is simplest, if not the best, solution.  The key is a smooth shank of appropriate length.  If the threaded section is too long, it can, of course, be cut off with a hack saw and groomed with a file.  To straighten out threads at the tip, spin a nut all the up to the shank and leave it on until finished with the grooming.

 


  

Joinery


The craftsman approach would be to use shouldered joints.  This is a link to the wikipedia page.




  

Pins


Solid Pins 


assemble with bolts
choose a nail size (diameter) and similarly sized drill bit for a snug (but not too tight) fit.  The match between the nail and the holes needs to be snug enough for good alignment, but not so tight as to prevent the joint from being disassembled by hand and the nails tapped out if so desired.
cut nails to length if necessary
drill two or more holes through one member and into the second member
tap the nails into their holes
Note: see @bib's answer for a "blind" variant of this    

Tube Pins


choose the bolts
choose metal tubing through which the bolts easily fit.   Note: as suggested by @AnonomousPerson in a comment, PVC tubing such as 1/2" plumbing can be used with good results for large bolts
in both members, drill through-holes in which the tubing fits snugly
cut lengths of tubing matching the members combined thicknesses
tap in a section of tubing
bolt together through the tubes 



  

Splines


Blind Rings


select 1/16" walled metal tubing whose diameter that is somewhat smaller than the narrowest member. For example, if the narrowest member is 2" wide, then select some tubing that is about 1.5" in diameter.
select a hole saw that matches the size of the tubing
temporarily assemble the members using bolts that match the diameter of hole saw's drill bit, typically 1/4".
disassemble
on each of the mating surfaces, using the bolts holes for guides, use the hole saw to drill 1/4" deep circular recesses
cut 1/2" long rings from the tubing 
assemble with the rings sandwiched in between
if larger bolts are desired, re-drill the bolt holes    


Blind Flats


same idea as blind rings but use 1/2" x 1/16" metal stock and saw-kerfs