There's much more to a Z06 than just the LS6 engine. It's really the complete package of suspension, transmission gear ratios, shot peened rear gears, improved clutch, front brake pads, the titanium cat backs, the thinner windshield and rear backlight, the rear brake ducts, shortend jounce bumpers, tires and wheels, dash guages, seats, front screens, and engine computer software that makes the Z06 work so well.
Yes you can build a LS6 engine from a LS1, but possibly your better choice would be to purchase the LS6 already assembled. That way your getting all the little differences that went into the design of the LS6 compared to the earlier LS1 engines. You still won't have a true Z06, but you will have one very good running 99 hardtop.
You also can purchase all the rest of the Z06 components and build yourself a fine handling Vette.
Of course it still won't be a true Z06, there's that little problem of the S in the Z06 VIN that will be a dead giveaway to the well informed.
But everything (except the VIN) can be accomplished with enough $$$.
However, if one is going to spend that kind of money, it would make a great downpayment on a leftover 2004 Z06, or a previously owned Z06. There's some real bargins out there to be had if you start searching.
Oh, to answer your original question on the differences, I'll just hit the high points: The LS6 Block has cast windows to relieve cylinder to cylinder pressures in the crankcase, (this also went into the later 2001 LS1 and all from 2002 and later LS1 blocks) the LS6 heads have 48cc combustion chambers to increase the compression ratio to 10.5:1, the 2002 and later intake valves are hollow sodium filled, the valve springs, again 2002 and later, are heavier, the LS6 pistons are coated to reduce friction, the cam is higher lift and duration than the LS1, the intake manifold on both LS1 and LS6 from 2001 and later are improved, the fuel injectors are higher capacity, the screen in the MAF was removed on the LS6, (this can also be done to the LS1).
Right off the top of my head that's all I can think of that's LS6 engine specific. Oh yeah, the LS6 redline is 6500 RPM, fuel cutoff is 6600 RPM.
vettepilot
Art
LS1-LS6 differences???? 
great summary . . . I have an 2004 coupe . . . My neighbor has a 04 Z06 they look similiar but now I can see the detailed differences
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