remember harder doesn't necessarily mean better and you might want to back off the damping on the shocks again before you drive it as "tightened right up" may close the valves and result in blown seals in your shocks...
my advice would be set them to about half way, make sure each side is the same, get the alignment done... from someone really good!... and go from there.
as for factory sways, they're there for a reason, I know you CAN remove them, but in general unless you know what you're doing and why then you're way better off leaving them in as you'll need to adjust a bunch of other stuff to make up for removing them.
I got my coilovers and new sways in and the car didn't feel as good either, and was VERY tail happy, took it to get it aligned twice and saw no real improvement.. only just got it all fixed. And if you're adding any adjustment capacity the standard suspension doesn't have, point it out to the aligner so they know to take it into account.
don't make massive drastic changed like closing off the valves in your shocks or removing swaybars before you've even got the alignment sorted or you'll probably end up breaking things, crashing, or making things worse.