I have been putting a lot of thought into the cold clipping stage (stage 3). Aside from the anode (plate) resistor change for stage 1, stage 3 would be the other culprit for fizz. At idle, the bias sets it almost at cut off. When anything more than (perhaps) a few hundred millivots comes in, it's going to be distorted and short on the positive side and within the headroom of the tube up to 4 volts (no overdrive) or 5 volts (overdriven, about to clip) on the negative side.
The issue is this: if a passive, high output humbucker is plucked and produces a .5 volt p-p signal and the Gain pot is halfway, the signal on the grid of stage would be about 15 p-p. So, the negative going cycle on the anode is clipping and has a nice distortion going on. The positive side can only get around a .25 volt peak (but will increase by a small degree, because tubes allow leakage). While tubes distort softly under most conditions, trying to force something 30 times larger than the available room is going to create a hard clip and square the output to some degree.
Further, when the Gain pot is turned up to the point that the fizz becomes very prominent, the low frequency response becomes blurred. That is also due to this stage. The filtering is cutting high frequencies off above 3 kHz and the cathode is not bypassed. The whole signal is receiving a very small, even amplification with the afore mentioned heavy distortion, which will make the low end lose focus, because the tube is affecting frequencies all the way down to 6 Hz. The amp has no grid resistor following this stage, so the resistance of the stage creates a divider with the 330 k load and passes more than 75% of the signal to stage 4.
While a cold clipping stage is going to produce harmonics which are mostly even-order (if there's no hard clip), the amplifying section of the next stage is going to amplify the crap out of the complex, harmonically rich signal, create more harmonics based of of the multiple harmonics coming in, and pass it to the cathode follower, while providing no filter for the treble harmonics being produced. Then it goes to the EQ, the PI, then the push-pull power section, which is going to produce odd order harmonics from anything it gets and will itself be fizzy, from the cold bias, if overdriven.
Now, let me say that this is exactly what the amp is meant to do. I would also argue that this stage is the heart of the amp and is a large part of its popularity. A person doesn't really need to turn the Gain pot way up to get a great distortion sound and is advised by Mesa to not do it. That's kind of point. Non-Metal players can use the tube rectifier to soften the sound, or switch to Spongy for a darker sound.
However, if a person wants to maintain the heart, but reduce the fizz and flub at higher Gain settings, a resistor change would be a remedy. I haven't figured it out yet, but if 10 k worked for a JCM 800, a value at or above 10 k is probably going to be a good compromise. Too low will change the amp too much. On paper, a value of 12 k to 18 k seems to provide a little more positive headroom and remain low enough to still work the way this stage is intended. I think the key is to get it just under the point of hard clipping. If anyone has done a mod to this section, please respond.
(Aside) As I mentioned before, installing a switch to remove the cold clipping stage would turn the preamp into something akin to a goosed Plexi. I still don't feel it's worth the bother in most respects, but if the bias mod has been performed, it could get a person close to the 6L6 equipped Marshalls, but in a modified form (or just flip the switch and install EL34s if the mod isn't done). Considering all the work involved and what it might do to the resale value, this might just be a mod for the person who plans to be buried with their amp. Otherwise a new design could incorporate this type of switching.