I made a jig to align the flanges:

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[Linked Image]

[Linked Image]

My original jig was just a piece of wood whittled down to fit. Or slap the driveshaft onto the flange and use it's holes to locate where to drill. No worries about centering since the lip in the center of the shaft fits into the recess in the face of the flange. An alignment jig is only needed when doing a flange-flange drilling.