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I'm trying to get the nvpmg to work. In halshow the inputs 1 to 9 are switching. But when the counts for the mpg are not working. Encoder.0. does not count when the mpg is moved. I have tried both input.19 -- input 25 and input 27 and 28 in the nv-mpg.hal but still nothing , should the switch be set the nv or std ? 

^^^^^
Have it sorted encoder inputs were on 20 and 21

Headers are already installed, and because of the kernel coming from the RPi GitHub repo, there are no Debian packages to suit the installed kernel.
will inform you of the info, including addresses, of all your network adapters.

If you could try that as well as the output of the ping command to that IP would be helpful. "It doesn't work" or some other statement along those lines without any additional information makes it very difficult and time consuming to help.

If the second NIC is for ethercat or a Mesa Card, I would use the on board Broadcom NIC for it and the Realtek card for internet connectivity.
The DKMS driver should exist for the Pi on Debian. You may have to edit /etc/apt/sources.list to add non-free to the Deb stanzas so it can find DKMS.
Worst you can do is break it again...
sudo apt update
sudo apt install linux-headers r8168-dkms

Hmm, Debian's wiki is as out of date as Linuxcnc's.

Untested, but I think the the correct way to bring a interface up should be:
ip link set dev enp2s0 up

So I think the interfaces file should be
pre-up /sbin/ip link set dev $IFACE up
post-down /sbin/ip link set dev $IFACE down

I did find a igc kernel patch Intel was involved in so I think its OK to ignore:Subject: [PATCH] net/igc: disable EEE by default on I225/226
>
> I226-V devices can hang when EEE is enabled. Explicitly disable EEE during
> initialization of the device, as the Linux and FreeBSD kernel drivers do.Also, I think we should disable all power mangerment in grub:
pcie_aspm.policy=performance pcie_port_pm=off

So many gotchas!

No, up to now I did not configure anything. I installed the Gnome network manager and plugged the network cable to the ethernet port. I got an information from my router that it assigned a new IP to that ethernet port, so I tried to ping on that IP.
As I wrote, I will take my time and try to read and understand how to configure the new NIC in Linux. I have worked with Linux several times in the past, but I am more a noob than an expert in Linux.

Have you configured the waveshare NIC to get an address via dhcpd ?
Have you done anything to configure that interface ?

Using dmesg gives information if I unplug and plug the network cable on eth0 and eth1:

cnc@linuxcnc1:~$ sudo dmesg | grep eth
[51259.808328] r8169 0000:01:00.0 eth1: Link is Down
[51334.956935] macb 1f00100000.ethernet eth0: Link is Down
[51336.323225] r8169 0000:01:00.0 eth1: Link is Up - 100Mbps/Full - flow control rx/tx
[51431.494868] r8169 0000:01:00.0 eth1: Link is Down
[51433.262584] macb 1f00100000.ethernet eth0: Link is Up - 100Mbps/Full - flow control tx

If I connect the port to a network switch it is getting an IP from the router, but it is not possible to ping to that ip. I will try to read some more about how to get that working.