I take it you haven't played through a stock 5E3 yet.

They only stay clean to "3" even with a 12AY7 in there., that's the way its been since 1955 or so.  There is almost no wiggle room between "On" and "Dirty' with the Volume knob; you are up to past "1" when the sound turns on and by "3" it's dirty and by "5" or "6" there is nothing but increased saturation.  So much saturation that any additional saturation from the 12AX7 would be inconsequential.  Many people find using 2x12AX7 in a 5E3 often makes it untameable and too hairy, you can't dial out enough gain to not clip the 2nd stage before the Volume control just cuts out (it's pretty useless between "1-1/2" and "0").  The 5E3 power amp is way too loose and flubby, especially on the low end, to keep the preamp tones from all mushing together.  People are always trying to coax more clean headroom from a 5E3, or at least some breathing room on the Volume dial; no one has ever been left wanting for more overdrive, if they do, then they have the wrong amp and need something hi-gain with a much cleaner, tighter power amp.   

Unmodded, a 5E3 is what is is...the darkest, loosest, most unfocused version of it's circuit, it's thick and raunchy and has a nice organic, rounded clean (admittedly only 12 watts RMS worth of it); but it's one step from being pure sonic mud.  There are plenty of mods to make it brighter and tighter and more controllable... more like a Brown Deluxe.

I like the 12ay7 in v1, using a 12ax7 would be unrewarding I suspect
But even so it's often mushy and there is little touch sensitivity.

I tried also adding a 12at7 in v2
This improved things a lot I think, I can get a lot of different tones, with a little more definition. Sag is still there, and whacked up full there are better tones there
I like the strat neck pickup the best, and this is improved a lot too with this extra change

Cheers
Tone