On alignment: I use jackstands and string touching the tires at hub level to set toe, front and rear. On my car the front track is a bit wider than the rear, so it does take a few minutes and some adjustment to get them straight. I don't need to tell you this, but always set camber first and toe last. Camber changes toe, but toe doesn't change camber.
On the clutch, you may need to tighten the slave a bit. Physically push the clutch cross shaft lever until you feel it touch the throwout bearing, then back off a tiny bit. That tiny bit at the slave will translate into almost an inch at the pedal. Are you using a 5/8" master and 3/4" or 7/8" slave? What is your pedal/MC pivot ratio.