Glad you got it fixed!
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I did look through the program code and found references to your errors but I couldn't find an obvious cause, only ways to patch past the errors. There are some diagnostic features built into the code but I haven't really explored these and there is a debug file that gets written to if anything fails during bootup. Yours has probably overwritten with a blank file if it is working OK.
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Note that the main program code includes a simulator mode where you can install and run the program on a (Windows 2000?) PC and it simulates a fully working E5052A. It even gives a simulated phase noise response on screen that has 'moving' noise.
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However, I tried it on a couple of PCs (not Windows 2000) and it quits after a couple of seconds. This may be deliberate as there doesn't appear to be a way to manually quite the E5052 app apart from turning off the instrument. I did manage to get it to stop quitting with a crude patch but it wasn't really worth the effort.
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The pass/fail limits for the various service mode tests are stored inside a file on the HDD and I can show you where this is if you haven't already found it..
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I'm pleased you got it working, I wasn't too keen on taking mine apart again and it's packed away in storage at the moment. It isn't an instrument I will use very often, maybe a few times a year or so.
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I've got an old library plot of an E8257D PSG sig gen at 1 GHz and it agrees very closely with your plot although the vertical scaling is very different.
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I can also see the 60kHz blip from the LCD on your plot. It's inverted but it will be much more obvious (and not inverted) when you test something with lower phase noise at a 60 kHz offset. You can see it in the plot below as well.
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