what am I missing. installed 0.6 mm nozzel  

RE: what am I missing. installed 0.6 mm nozzel

I ran the calibration from the beginning again,  and I had to adjust the z access a lot more than I anticipated.    Got it working.   

In case anyone comes along trying to do the same thing.  

I set the nozzle size to 0.6 on the printer and also in the gcode I am using. 
My suggestion - after the calibration,  print the Prusa test pattern and use that to Live Adjust Z to get  Z dialed in.  

1) the border of that print will let you know when you are getting close.  Once it lays out a clear border, that sticks all the way around.   you are close.

2)  once you are that close, when its printing the rectangle that will say prusa,  adjust the z approx 1/3  of the way and 2/3 of the way through the rectangle.  
This allowed me to get it dialed in quickly 

RE: what am I missing. installed 0.6 mm nozzel

Is this something you're seeing in actual prints or just the first layer calibration? Try to print a calibration strip like this https://www.prusaprinters.org/prints/105404   instead of using the inbuilt calibration routine.

In the gcode I changed the nozzle to 0.6.   

Not sure what that means. No need to change gcode. But you need to run the Prusaslicer configuration assistant from the Configuration menu again and add the Mk3S+ 0.6 mm printer profile, which will configure everything correctly for you. 

RE: what am I missing. installed 0.6 mm nozzel

First, read:  

• https://help.prusa3d.com/article/different-nozzles_2193
• https://blog.prusa3d.com/everything-about-nozzles-with-a-different-diameter_8344/
• https://projects.ttlexceeded.com/3dprinting_nozzle_topics.html

One last setting you will want to do:

• In the menu on the MK3S:  Settings: HW setup: Nozzle d.