The 'vettes since about '98 are pretty bullet proof.  It's a hell of a lot of money for what you get.  I've got an 
'02 Pontiac Firehawk that's got pretty much the same engine detuned (345 bhp/345 ft./lb. torque).  It's my "good" car.  The Boxster is my daily driver.  The LS1 is one hell of an engine.
Having said all that, the Boxster is a great car too.  After doing the rear speaker install, I can't help but think, "Why doesn't GM buy a Boxster, take it apart, and see what makes German engineering so great?  It's is a damn well made car."
But, at the end of the day, you've had a Boxster.  It's time you get the Z06.  At worst, you can decide that you made a mistake, sell the Z06 and buy another Boxster.  Right?  
I can tell you that nothing brightens your day quite like putting the pedal to the floor on an LS1.  The Boxster goes great.  It's a great car.  In terms of straight line acceleration though, it can't touch the 'vette.  The Z06 probably has it in cornering performance too.  I think the Boxster shines in braking though because of its lighter weight.
If you have any doubts, just listen to it (
60-120.
One thing I know is very different between the Boxster and the LS1 is the power band.  The LS1 has a much narrower power band than the Boxster.  You have to drive it much differently as a result.  Besides, try to get 28 mph on the highway in a Boxster.