... if I wanted to perhaps try just a couple of the SLN tubes to see if they start to lower noise where would be the best place to start? As follows:
1st gain stage (pair)
2nd gain stage (pair)
output stage (single)
While I'm not familiar with the internal design of the VTPH-2 or 2A, and I've never taken the cover off of my VTPH-2 (having seen a number of past comments which like Jmolsberg's comment above have described finding tube rolling to not provide much if any benefit to Keith's phono stages), my guess is that if you want to give it a try the first gain stage would be where to start. Especially if that is where the 12AX7s are used. (I don't know if the 12AX7s are used in the first stage or the second stage).
Since signal level is presumably lowest in that first stage any noise generated by that stage will degrade signal-to-noise ratio more than it would be degraded by a similar amount of noise generated further downstream. Also, it may be relevant that the 12AX7 has a higher intrinsic gain than the 12AT7.
Good luck. Regards,
-- Al