One thing you might want to consider if restarting from scratch is to install using the 73-Linux tools but only installing a few items at a time. You have already identified that certain apps need to be installed in order for them to work properly. I think the scripts account for that, but you can force it by only installing the earlier apps, running and configuring them, then installing the next, rinse and repeat. Verify flrig is working with full control of the radio, probably with fldigi, before installing direwolf by running 73-Linux again, edit direwolf.config before running it the first time, then install wsjt-x, etc., rebooting the machine after each install. There obviously are interactions between these packages. I don't fully understand all those interactions, but I have noted that making sure each package is working before moving to the next seems to help get the interdependencies resolved correctly.
It's somewhat painful to add the next level of protection, but it might be worth it - get a full backup of the system between each install after ensuring the last package is working correctly. If the next one fails, you have saved the work up to that point and may not have to go back through all those steps again.
