First layer height problem after changing nozzle
this is a common case in my TT....
Please check the y-carriage wheels - on the 2040 and 2020 profile.
Mostly you shall find a little wobble on one of the ends, that introduces instability in leveling, so you could level it, home it and another level is needed. 
In my case, I decided to upgrade for dual-z drive - please see this

Another interesting Z upgrade:
option two

We can observe z-wobble by watching the x-axis on the left side (no lead screw), it will have a little delay in response when moving up/down comparing to the other side.