The sides to front misalignment could, in addition to a not perfectly round collar and/or not perfectly centered bit, be caused by a parts orientation error. If the reference faces, (the face either visible or down/up against the jig) are flipped on the drawer sides, relative to the reference face on the front and back, slight centering errors can pop up and they'll be consistent - wrong but consistent.
When you do half blinds on an overlay drawer front things get a little trickier because the center of the drawer front is at a different distance from the reference EDGE of the sides and back.
Do the sides and back line up properly and it's just the sides to front that are off?
As for the dado cuts - there's a slot cutter bit that I've seen ads for that let you route the dado for the drawer bottom after the drawer is assembled - but not glued yet (obviously) With an overlayed drawer front drawer you'd have to figure a way to raise the sides and back to get the drawer bottom edges parallel to the router table top but that can be done. Anyone use this slot cutter bit for this purpose?
charlie b