Hi Oli,
Just a couple general comments: you have a LOT of driving and road conditions can be trying. You will have to drive a lot at night to leave yourself sufficient time to bird, in my opinion.
Some more specific comments:
The Owlet lodge trails are perhaps not necessary, the Puente Sin Nombre trail opposite and a bit below the lodge has Chestnut and Leymabamba Antpitta, Johnson's Tody-Fly along the start of the trail, Emerald-bellied Puffleg and more.
Aguas Verdes and Arena Blanca are sort of the same thing. You can bird a few kms uphill from town along the road but mostly the same birds as you will find at the reserve, I would bird the reserve and if you're missing something key bird a bit above town on the way back to Affluente/Elmer's Llanteria.
For your Tunnel / Koepcke's day, the metal tower past the Koepcke's spot is probably the best stakeout anywhere for Dotted Tanager, and is good for Plumbeous Euphonia.
Upaquihua is excellent, can get everything there without going to Juan Guerra, and I suspect you'll see more concentrating on one spot and not rushing so much. Upaquihua is worth getting to early and spending time, lots of good birds and some can take a bit of time.
I would recommend staying at Waqanki and birding there more, one of the best spots in N Peru, tons of specials to be found. Morro Calzada is not a necessary stop and there have been robberies, might be best avoided.
There is a stop near La Rioja for Pale-eyed Blackbird and Black-billed Seedfinch.
Your drive through the Balsas looks aggressive time wise, it's a long drive and while paved, is very, very windy. It's also very scenic. The birds can be tricky, surprisingly, particularly the Parrotlet. I might suggest bird from Leymabamba to Abra Barro Negro and then start down the other side and camp, continuing in the morning, rather than trying to do Leymabamba to Celendin in one day with the birding.
You'll see a lot no doubt but you are going to miss tons of the hard birds and endemics on such a fast schedule. Just up to you how much variety you want to see vs seeing more of the birds from fewer locations.
Sounds like an awesome trip either way!