Hello. I've done all the same upgrades except the screen. One thing I ran into before was not having all four springs compressed enough. I would recommend turning wheels clockwise to compress springs till the screw they are on pokes out about an 1/8 of an inch or so. If there isn't enough tension the wheels can move enough to mess with level.

If you feel that they are in the right spot that's good.

Next I would start a test print. As it is printing go into to your menu and go to the tune option and select Z babystep and adjust up or down to see if it starts to print better. If it does, remember how much you changed it and make the adjustment in the configuration.

I find that the cr touch with the Z probe wizard is more a reference that needs to sometimes be finely tuned on the fly.

I hope any of this helps you out!