Just a few points concerning the upgrade, a couple which are relatively important...

• Upgrade of the license server went fine although it might be an idea to note in the documentation that the UIM server needs to be stopped first.
• Upgrade of the EE application went fine except for one thing, all previous configuration options decided to disappear so you're basically starting with a clean system. Presumably this happens during the upgrade of the Derby database and luckily I knew what I had configured although I suspect if you have made a lot of configuration changes you wouldn't be too happy
• I need to make component images at both a dataset and volume level from both z systems and ZD&T systems. To do this you need to set-up a connection to the z or ZD&T system which requires IP/user/etc. The first attempt results in the following message:

 Linux command /usr/lpp/IBM/zdt/feuc version was not found. Error message: stdout: , stderr: /usr/lpp/IBM/zdt/feuc: FSUM7351 not found

However this is because you need to install the relevant tools on the z or ZD&T system first as described in the User Guide (perhaps also pointing this out in the relevant chapters, i.e. 'Creating Application Images'.) 

This duly done, the next error message is:

The ZD&T extraction utility running on z/OS is in a version older than 12.0.1. Please upgrade to the latest version.

Which is very strange as I had just upgraded to that and downloaded the SMP installables from the EE server. Double checking the EE server gives me:

ii  zdtapp                                1-12.0.1.0.20180828201436          amd64        ZD&T EE Web Application, version 12.0.1.0.20180828201436 , build date - 08-28-2018 for Linux on Ubuntu 64bit

So I have upgrade and therefore this looks like a problem with the SMP installables. In fact looking at the version date and the dates of the z/OS executables might be the reason:

20180828-201436

20180813-0912330198

Sebastian