Some players have problems getting enough headroom out of the Vibro-King, especially when using a guitar with humbucker pickups. The VK is an unusual Fender amp - you can't just set the knobs the way to what you use on every other Fender amp.
Remember that the VK has more gain than most Fenders. The trick with humbuckers - at least for my preferences in sound and feel - is to lower the guitar's volume a bit while cranking the amp's volume.
I don't raise the amp's treble to compensate for the hummers. The VK is pretty bright sounding as-is, which brings quite a bit of sparkle to guitars that might seem a bit dark with other amps. In fact, I often roll off the guitar's tone control for the bridge pickup just a little bit if I find that there's too much of a sharp edge on the sound.
Humbuckers put out a lot of low-end, and can be a bit scooped in the midrange. So you have to be careful not to run the bass too high - I open the bass just enough to give the guitar a "full-bodied" sound. Raising the mids a bit helps, too.
When I plug in a new humbucker guitar, I start with volume, treble, bass and mids all on 4. Generally, the treble will go a bit higher and the bass a bit lower, per my preferences and mood. If I'm going to be playing totally clean, I might drop the volume a bit. But with every humbucker guitar I've tried, it has always worked best to roll back the guitar's volume control.
One trick that I use to get a bit more headroom out of the VK is to raise the treble control and compensate by reducing the treble on the guitar. This works well because the VK doesn't get glassy or brittle at higher treble settings.
IMO, a strong high end is a good thing. That's where all the note articulation lives. Don't neglect the fact that your guitar has a tone control that can help tame those highs. I run my Kritz (single coil) with the tone rolled off a bit almost all the time. Plus, it's nice to have that extra bit of treble in reserve for when you want to roll back the volume a bit and thin out the sound, or when you need to cut through cymbal wash at higher volumes.
I've tried input #2 a few times, and don't like the way it "dulls" the sound of the guitar. Rolling off the guitar volume a little helps to overcome the excess gain without squashing the high mids and treble. Of course, with the guitar volume rolled off a bit, you have some room to adjust for picking intensity. And for a great solo sound, just roll the guitar volume to full-on and dig in a bit harder with your picking hand.
If you've done all you can with the controls on the amp and the guitar and there's still a big gap between the headroom you have and the headroom you want, then it may be time to consider whether the VK is really the right amp for you.
If the headroom is just a little bit short, then you can probably be happy with just speaker and tube changes. The alnico-magnet speakers are inefficient and break up pretty early. (For what I like to hear, that's a good thing.) Replacing those speakers is one quick way to improve headroom. You can also try swapping V4 for a 5751 or 12AY7 to reduce the gain a bit if it seems like your pickups are just too hot for the amp.