I’m still working on my example (and it will need to be reviewed by some other people before it’s ready to post) .I sorta stopped for a while when I realized it was impossible to completely erase your resonance signature. Also, an example isn’t going to simplify things, the way to simplify things is to talk to your GM on how you want to house rule the matrix.
For stealth, the way I have seen it done is the node makes a threshold stealth test when you hack in (as noted in hacking on the fly or probing), then if IC is running with the Analyze program, it can make Pilot + Analyze vs. Hacking + Stealth opposed checks to detect you. If it fails, it can try again every action with a -2 penalty.
Never really used nuke. If the node reboots you will have to rehack in
