Putting KT88s in an amp designed for 6L6s or EL34s could be trouble. KT88s are a very high output tube design - you may run into trouble with the fact that Mesa amps are fixed bias. Ideally, you should find someone with a tool called BiasRite to see how the tubes are operating. You may need to go through several pairs of tubes to find ones that have acceptable performance in your amp. Putting a quad (or 2 pairs) of KT88s in your amp blindly could lead to output transformer death.
If it works, it may not get you any closer to the tone you're looking for. I have a VHT with KT88s and in my experience, much of the tone comes from the preamp circuitry, rather than the power amp. Until recently, KT88s were primarily used in high-end audio amplifiers where distortion is NOT desired. So you really have to crank the hell out of them to get tube distortion (which does sound killer). I read an article by Steve Fryette of VHT where he said that most of the power amp distortion actually comes from saturating the output transformer. Which explains why low-wattage VHTs (like the D60) can get great power amp distortion at reasonable volumes.
If you're going after an Isis-type sound, one thing to consider is that not all VHT amps use KT88s. In fact, some pittbulls (the CLX) use EL34s. The ultra-lead that (I think) Aaron Turner uses can be run with either KT88s or 6L6s.
Instead, my advice would be to try a VHT cab. They have a very particular sound. Also, try turning the preamp gain/drive way down on your recto and don't scoop the mids (perhaps even slightly boost them). Then turn up the master output volume. Isis uses a lot less preamp distortion that most people think.
