Hi and welcome to FlyerTalk!
Arriving at 2pm is more than enough for a 540 departure. More so, I would actually book Lan's 420 flight to Cusco. In the unlikely scenario that your flight from Pucallpa is delayed, Lan can put you on the 520 or even the 540 flight you mention. Note that upon arrival in LIM you would have to go to check in counters to get BPs for Cuzco. Even so, 2 hours is more than enough and therefore, you could safely book in advance.
If you have not booked your Pucallpa flight yet: book everything through the same carrier. PCL-LIM in the morning and LIM-Cusco right after. That way you can have BPs all the way from PCL to Cusco and make matters much simpler.
Good luck!