I have also upgraded from Angular 5 to 6 and I had the issue when building for universal. What I did was to download the sample app from the angular universal wiki and compared the files that I have with the ones discussed on the wiki.
It could be so many reasons why the build won't work for example, I have noticed one of my mistakes was with the script
"build:client-and-server-bundles": "ng build --prod && ng run MY-APP-NAME:server",
I had copied and pasted the one from the wiki but the name of my app was different. I have corrected this as my previous script was still using the --app which is no longer used but we now scope using --project as you can see the change in the new angular.json file which has a property of projects instead of apps.
Another thing could be that in your server.ts file you still have
const { AppServerModuleNgFactory, LAZY_MODULE_MAP } = require('./dist/server/main.bundle');
instead of
const { AppServerModuleNgFactory, LAZY_MODULE_MAP } = require('./dist/server/main');
Thus the best way I have solved this issue was to follow exactly what they are doing in the wiki and also compare the package versions they are using and updated mines to match their packages in the package.json those that are concerning Angular
Hope that'll help