1) Next time can you make a mount for your faceplate on the rotab and mount your workpiece on the faceplate for the lathe operation. Perhaps making a range of faceplate dogs that make it chuck-like.
2) Use a centre drill to pick out the hole positions and then open out on the pillar drill. If not enough room even for this mount a dremel-like additional spindle on the Centec head to hold the centre drill.
3) make a mount for the rotab on the back of the lathe spindle, yes it has been done before, so you can spot the holes on the lathe.
4) mount your pillar drill so it can be swung over the mill table with a bit of extra bracing to firm it all up.