Specifically looking for precautions/suggestions about whether or not to bring that new digital SLR along. Most of trip will be in Cusco, Inca Trail, Amazon. Only using Lima for international flight. I realize its a calculated risk, but seems crazy not to bring my best camera on this dream trip.

Ricky,
We had no problems in Peru. As you probably know, it's best always to keep a close eye on your stuff.
The Inca Trail is tough! We only did the small section from kilometer 101 and it took most of the day.
Would recommend one of the Titicaca boat tours out of Puno which includes an overnight stay on one of two islands in Titicaca. (Also, see if you can get you boat captain to stop the boat and let you jump in!. It's quite refreshing!
Enjoy the finger puppets!!
Travel Chic

I've taken my digital SLR all over Peru and never had a problem. Keep it in a non-descript backpack (not one that screams expensive camera bag), don't let the bag out of your sight, don't anyone's offer to take your picture, and lock it in the hotel safe when you want to leave it in the room. It will be fine.

If you are only using Lima as an overnight stay I would not worry too much about crime ,as you will be leaving early the next morning for Cusco.

The Inca trail is not easy, and has been mentioned you might only want to do a part of it ..just to get the flavour.
It takes 3-4 days to do the trail.

The Amazon is hot and humid, when I was there in March,it was 102 F when I landed at the airport in Manaus.

Take your digital ,I took mine with no problems, of course you will keep an eye on it always.
Percy

You should have no problem on the Inca Trail. When in Cusco just take precautions and be aware of your surroundings. Make eye contact with any suspicious-looking folks hanging around so that they know you see them. Enjoy your trip!