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Drilling the holes is the hard part. I considered lathing a piece with the correct taper and a flat on the top, then heating the pipe to make it moldable with a heat gun and pressing it into an undersized pilot hole. This is more likely to work, especially if you use a drill press and clamp the pipe to make sure its really straight. I just drilled the holes with a 5/32's drill and tilted the drill and spun it around (at about a 30 degree angle). Try to keep the holes round instead of oblong, it will make them seal better. Use a piece of scrap pipe to practice and test with a spin column. Also test with a spin column regularly as you go. Remember that you do not have a magical drill that can redrill a hole smaller, so when in doubt, drill a hole small. Also, the spin columns wear out when you put them into and take them out of holes, so a spin column you use a lot will fit tightly in a hole that's too small for a new spin column.
I leave how to plug the extra holes as an exercise to the readers. I'd suggest tape, you could probably find non porous plugs as well.
Setup difference between this and the Qiagen manifold:
This drains fluid into the vacuum tube, the Qiagen manifold stores fluid in the manifold and you can drain it out a capped hole on one end (the cap that leaks on ours). This means that you must have the manifold hooked up to a waste flask that is designated for QIAGEN waste (remember that mini and midiprep waste makes chlorine gas when combined with bleach). This also uses a 3/8" inner diameter hose, I think the Qiagen manifold uses something like 1/4" ID.