personally, I get a descent DLR-era tone with guytron GT-100 with its silverface settings when recording cleans in a studio. For distorted sound when using the same amp, frontside controls on B channel are all at 1400 hrs with gain and mids at almost 100%.
When I used to play in a cover band and we played a lot of alcatrazz and DLR songs that Vai recorded and then I used 5150 II, all settings at 1600hrs but treble and presence at 1100 for songs like yankee Rose, Shy Boy, Goin' Crazy, Skyscraper, Hot Dog and a Shake and Hina. For Stand Up, Ladies' Nite In Buffalo and Big Trouble I was not using amps dist section but was playing throught a clean channel with a custom-made OD pedal (almost identical to CMATMODS Brownie that you can get nowadays from Chad Matthews - it has almost the same tonal color as 150 has but a much rounder edge so it doesn't "bite" as much as 5150, its more "classic" tone). I was using LNG and EBMMEVH both with stock pickups but EBMM was strung with 11s which made id harder to shred but I could get much richer tone for the cleans.
On the other hand, I was never obsessed with a certain guitarplayer's tone and was not chasing it no matter what, I'm always rather looking to other guy's tone as a guideline for my own.
Nowadays I either use lince6 X3 live if I play in a venue that has crappy amps so its much better to plug straight into PA or I carry my Guytron 20W combo and my pedalboard with 3 different OD stompboxes that I use for a different ammount of distortion in my signalchain. My current band plays everything from original to rollingstones to 80;s rock and glam to electric six to korn. Tonewise, I got stuck in the 80's and my favourite is EVH with his cranked marshalls and Vai on Eat 'em... and Passion and Warfare albums. If we play big venues with 200+ people I usually take my 5150 and 3 guitars - either JEM or EBMMEVH, strat and one of my lespauls (either custom 1969 or Boneyard), if we play smaller venues then its 20watt combo + pedalboard for some variety in tonal "colors".
But the bottom line is, as IbanezFreak777 said - fingers, fingers, fingers. I was very close to his sound with the rig I had then but I was soundling like me trying to play like Vai