I agree with your assessment. The harmonics are the larger issue, and need to be addressed. Changing to the shielded inductors before and after the 45 MHz crystal worked for some, and is a much easier repair than changing out the 45 MHz if transistors.
The only issue with the above is that you do need a way to measure the spurs. The harmonics are easy and can be done with either a separate receiver or a low cost spectrum analyzer (SA). I have found that measuring the spurs is more difficult, as you need a better RBW (resolution band width) SA to do so effectively.
(asbestos suit ON)
I would assume that it would be of interest to this group to post a how to verify the issue with minimal equipment. Having been a retread ham after 31 years away from the hobby, and starting with only a vom and cheap oscilloscope, I can identify with the issues that some might have with testing. I did not have another receiver to test the uBITX with, and was not a member of a club when I first built the uBITX. I found out afterwords that there were emission issues.
I have since made part of my hobby to add the more test equipment, however I still do not have what I would call a good spectrum analyzer. I have tried most of the low cost alternatives that have been listed in this forum (it is fun to test them out and not too expensive to me). As stated above, I have found them to be great at one type of test or another. None seem to meet all of the needs to vet out the uBITX. I have just recently received the Antuino, however have not had the time to go back and redo the spurs testing.
The last point is that I would feel safe with sticking with the low power of the bare uBITX in working SSB on all bands. The reasoning is that the 10 db of attenuation missing with the spurs is way below a similar rating for a 100+ watt rig. The risk of interference is small. I would only use it for CW if one of the low pass filter modes was done, as the harmonics are much higher and in general CW is a lower power mode. I would not connect the uBITX to a power amp without vetting the signal purity.
As always, the above are my observations and opinions. You will need to verify for yourself.