I just did the exact same thing! I replaced all of my 12ax7's with spax7's. My gain, dead, clean? Dead. Tone? None. I took them back and ordered 5 stock mesa tubes instead, and put my old tubes back in which are V1-Stock Mesa, V2 and 3 EH 12ax7, V4 and 5 stock mesa. I wanted to try a JJ as well, so I went out and bought one. I just threw it in V1. It's an ECC83S which is the standard 12ax7 replacement. I tested with my epiphone flying V that has a Duncan Distortion pick up in the bridge position. This guitar has an unreal bass response. It can actually be way too much when I have lotsa gain pumping as well. I also tune down to B, so when I play on the lower string, the bass is even more present.
Onto the JJ's sound in V1. My clean was great. Really nice and organic. I had been having a problem with higher notes on the unwound strings being too shrill, and causing a little ratty over drive. The JJ smoothed out the shrill highs without actually killing them. The notes were clear, clean, and precise. When I switched to my neck pick up (an epiphone design based on a P 90), I was greeted with an ultra warm tone that was very smooth. What about high gain? In my modern channel, the JJ did not hold me back. I noticed right away that there was a little more string separation, and a tighter bass response. This was with the gain set around 2:00. So, I did the only logical thing, I cranked that gain baby! Rectos have sick amounts of gain, and when cranked, typically lose a lot of note definition. While I lost a little definition, every chord and note I played still maintained a nice separation. I also noticed a more "wooden" sound coming through the amp as well. It seemed that the response was quicker as well, and notes had a little more punch than before.
I don't know if I will retube my whole amp with JJ's yet. I am still waiting for a couple of NOS preamp tubes to try. I have promised myself that I will only buy these 2 NOS tubes and thats it. Too much money. After playing with this single JJ preamp tube wasvery cool, so I will probably be calling up Bob at eurotubes when I am ready to do a retube. I also want to see what this JJ is like with stock Mesa tubes as well. So many things to try, so little time.
On a side note, when I took back the SPAX7's the guy told me that they "were not low gain, just a better spec 12AX7", and that "Pre amp tubes don't influence tone that much". Interesting...