how to drill aligned holes in steel pipe?
Looks like this project has two main issues - getting all the through-holes in the same plane on the pipe, and making a straight hole all the way through a pipe.

To draw a straight line on the pipe, you can set the 2" pipe on the flat ground (like the floor of a garage) and place a common (straight) 1x4 board next to it.  Run a marker along the corner formed by the board touching the pipe and you'll have a straight line.

For drilling the straight holes, you can either buy a drill press (random example) or you can make a jig.  The drill press is pretty self explanatory, so here's an idea for a jig.

 Drill bit
   !
  _!_ top plate
 | ! |
 | ! |
 | ! |
 |_!_| bottom plate
 |/ \| - hole for pipe
_|\_/|_ footing
_______


Now, with my amazing artwork out of the way....  You make this structure with some 2x4 lumber and use a steel plate (thin is fine) on the top of the "top plate" and "bottom plate". The total hight of the jig will be about 11".  The square at the bottom should be just big enough for the pipe to fit in to keep it centered.  Get a 12" long drill bit and drill through the jig as straight as possible measuring as much as you can.  This pilot hole will make or break your jig.  The steel sheets/plates will help keep the bit centered over the long run but are optional if you don't have many holes to drill (the wood of the jig will waller out after repeated use). If you can get a perfectly straight hole, you should be good to go!  insert the pipe and get to drilling.