That extra info is good!

For the drilling, you need an A-axis, if you want the material turned automatically. To begin with, as you're only drilling holes on opposite sides, you could always just rely on turning the pipe by hand (machine drills/machines one side, then spin the pipe 180deg and let it do the other side).

However, now that I know the type/size of holes you're doing, a x and y axis is pretty much essential.
For the bigger holes, in order to keep the edges parallel, you either need to use a milling cutter and move the work under the cutter, which requires 3 way movent (up/down, fore/aft, right/left), or to rely on having the correct sized cutter so the pipe remains stationary.

The hardest part I'd say to design, will be some form of clamp/support for the pipe. Rotary table at one end with chuck to control rotation of pipe, then on the moving head, some form of roller/guide assembly on the head to support the pipe at the cutter (probably one either side of the cutter for maximum support).