Malmsteen Tone and tone in general
The JTM 45 amplifier was the first Marshall amp and was based on the Fender Bassman. *Eric Johnson also has used this amp, as it gets a very warm, musical distortion. *This is one the rare amps still made today (the reissue) that actually uses a tube rectifier and isn't a boutique amp. *However, you must definately turn these amps up all the way to get that tone.
As for your master volume amp, most audio-philes hate master volume amps in general, but yes, you need to crank it to get the best tone. *If loudness is a problem, I would suggest going with a lower wattage. *But more importantly, you should check out a power attenuator like the THD Hotplate.
Malmsteen specifically uses the 1971-1972 era Super Leads though, which are indeed very loud. *As for an SRV tone, you will want some kind of genuine Fender amp with original circuitry, like a Blackface Super Reverb. *The Ibanez Tube Screamer is also important as it fattens and warms up the sound. *All of the elements of his setup combine to be important, like the rosewood board, huge frets, huge strings, etc., but maybe the most important thing was that his pickups were rewound at the Fender factory. *So in this respect, I think the Texas Specials are the closest reproduction. *For a smoother Fender sound, maybe try a Deluxe Reverb with a nice chorus pedal and warm analog delay.
In any case, your technique will far outweigh the equipment you are using. *Think of what tone you are trying to get and then tweak your equipment and playing style to get that tone.