I think you gave the rig enough burn-in.  I agree with much of what you said about the fixes and sound as well. 
 
I find the EF5/HE-5 combo actually sounds better with my $99 uDAC than my $699 PS Audio Digital Link III, which makes the HE-5 warmer and fuller sounding with the EF5.  At first I didn't like that DAC with the HE-5/EF5 but it grew on me.  I suspect I would also like the EF5/HE-5 combo with my Mini-DAC and I'm going to swap DAC's between my bedroom rig and main rig later, since I think the WES/O2 Mk1 sounds a little better with the PS Audio in terms of frequency response. 
 
Now, with the PS Audio DAC I prefer the HE-5 with my WA6 over the EF5 amp, and with the Apogee/ZDT I like the HE-5 more as well.  So, I wonder if changing the tube in the EF5 will help us, or if trying a different source (or amp) will help you. 
 
At this point, with the ZDT and WA6 amps I liked the HE-5 enough to sell the APS V3 RS-1 and TTVJ portable Millett hybrid to plaidplatypus (medical bills and car repair were calling).  So, you'll get to hear that at a Florida meet one of these days.  I have not extensively compared the HD-5 to my LA7000 yet but I suspect I'll find them to be on a similar level, making the used price I paid for LA7000 much less painful than full price.  Was your wife liking modded D2000 or D5000 more?