Is my new amp TOO GOOD?

Is the unit broken in? Often this is what a new component will sound like before it is fully broken in. Allow at least 200 hours of play before starting to draw conclusions if you have not. 

Also try repositioning your speakers. You can often soften the often hard Beryllium tweeters. 

Hopefully it is not actually distortion. 

Too good...no. That is not how it works. Now you could have upstream components that are harsh and they are being better conveyed. Then it will be a mater of correcting that. 

Sorry, that’s frustrating. You should be experiencing the joy of your amp upgrade right now - and upgrading in the same line - that should have been an easy win! Speaker & amp matching can generally be pretty persnickety if you’re not willing to incorporate heavy EQ, especially with beryllium tweeters in the mix. But then you’re already doing some light EQ, and that should have helped enough.

Since you have a tube preamp, I’d be tempted to slam in some warm & thick sounding Mullards and see if that helps (vintage is best but even the Russian reissues are warm). You could try to toe-out your speakers a  bit, too. 

There’s also always the chance something simply got connected / setup wrong in the new mix. Maybe do a round of disconnecting and reconnecting every cable & component?

If you did the upgrade program I’m assuming you went through a Mac dealer.  I’d be talking to the dealer or Mac directly if you haven’t already, and if you have what do they say?