Hi, Skartalov
In the Projects Window, Select the Layer you want to delete, Then right click on it and select Delete, Work's Hear.
The Ooops button will bring it back, Hear also.
Using ver. 3.00.2
For the tool change Issue, I'm Assuming this is a "Manual Tool Change" Hear.
Hears a LazyCam post to try, Put it it your Mach3 folder, Load it as your LC Post (Instead of the Default).
You will need to setup your "G28" Home Tool Position in Config, Homes & Limits, X, Y, if needed and Z to your 5.0 inch value for tool change.
It seems to work fine Hear, Test It First, Please.
You can Edit this LC Post with a Text Editor.
Hope this Helps, Chip