No, I understand just fine. Again, 2007 or 2009 doesn't really matter, that same "Universe" engine is still there and in addition to that there's now the overhead of the DB2 repository and the IIS and WAS servers on top of that. It's good that you got "bigger and more powerful boxes&q...
There are a ton of conversations here on the topic of that -14 or "Timed out while waiting for an event" error. Have you been through them? What solution was offered that there's a problem understanding? I'm assuming it was something along the lines of "run fewer jobs at the same time...
What 8.x version do you have? There is something new in 8.1 (from what I recall) that will allow the generation of a surrogate key with a call to a new function in the Transformer stage. There's also this FAQ posting if you want to do it in a manual fashion.
:? Since you've started a new topic and have not posted an actual error we have no idea what "solutions we have provided" nor what precise issue you are fighting other than things apparently "stalling". And the assertion that "Universe has been removed from the 8.1 framework...
You're not going to want to trigger the job directly from there unless you're willing to simply launch it without waiting for it to complete or being able to monitor its success or failure.
Just how tightly coupled do these processes need to be?
And as well, anything with a 'Backup' option like hashed or sequential files will have their backup restored, in essence resetting them back to their original state as well.
So, one typically takes a 'two pronged' approach - backup everything (Engine, projects, the works) at the filesystem level and also take exports of all projects. With those you should be able to recover from pretty much anything.