Hi Lewm,
Intrinsic noise is not important if a tube is used at high signal levels. It is only important in the first stage of an amplification chain, where it can set the signal to noise ratio of the system.
You mentioned that you use the ECC99 in the first stage of a phono preamp, as the upper device in a hybrid cascode. In that location, intrinsic noise would definitely matter, although not as much as the lower device in the cascode. The ECC99 is a good performer, within a couple of dB of the best current production tubes I've measured.
I've updated the project page on my website again, to include the actual noise measurement histograms for the JJ 5751, JJ E88CC, and Tung Sol Reissue (Reflector) 6SL7GT. It is interesting to compare the three different plots - they tend to suggest that JJ is having some trouble getting consistent noise performance for their E88CC. The JJ 5751, on the other hand, shows fairly tight distribution and pretty consistent low noise performance.
Scott