I need some help with a Peru itinerary that just isn't working

So I'm going on my honeymoon soon had the whole tripped planned out, except that I didn't actually book very much yet. When I go to start booking things I realize there are some travel issues that just aren't working out in my favor. Specifically, I found that flights directly to Cuzco from Arequipa are only at 8 am and are only every couple of days. The only other flights go back through Lima and have really long layovers. My backup plan was to bus from Arequipa to Puno and take the train, but the train also only leaves on certain days and only early in the morning. I can deal with this, but it really messes with my itinerary. Here is the original plan:

Friday Day 1. (flight) Home->Lima
2. (3hr bus) -> Paracas
3. Paracas
4. (bus) Ica/Huacachina -> (overnight bus to Arequipa)
5. Arequipa
6. Arequipa
7. (bus) Colca Canyon
Friday 8. Colca Canyon
9. (bus) Arequipa (flight) Cuzco
10. Cuzco
11. Cuzco
12,13,14,15. (trek Inca Trail) Machu Picchu
Saturday 16. Cuzco
17. (flight) Lima->Home

The plan breaks down on Day 9, because there is no flight to take. Instead, the only flight is a day earlier at 7:30am, which means I need to be back in Arequipa on Day 7.

That essentially cuts Colca Canyon completely out of the trip. I end up spending 3 days in Arequipa and then 4 full days in Cuzco before departing on the Inca Trail, which I already have my tickets for. So now my itinerary looks like this.

Friday Day 1. (flight) Home->Lima
2. (3hr bus) -> Paracas
3. Paracas
4. (bus) Ica/Huacachina -> (overnight bus to Arequipa)
5. Arequipa
6. Arequipa
7. Arequipa
Friday 8. (early morning flight) -> Cuzco
9. Cuzco
10. Cuzco
11. Cuzco
12,13,14,15. (trek Inca Trail) Machu Picchu
Saturday 16. Cuzco
17. (flight) Lima->Home

This is a bummer to me, because I don't know if Arequipa is worth spending 3 days in. I don't know if Cuzco is worth spending 4 days in. And I kind of wanted to see Colca Canyon. So now I'm a bit lost on what to do.

I'm considering these changes:
1. Spending just 1 day in Arequipa and leaving on day 6 to take the bus to Puno. Spending Day 7 in Puno, and then taking the Andean Explorer train on Friday to Cuzco. That will still leave me with 3 days in Cuzco. But I'm not sure if my fiancee will be up for it because thats a lot of traveling between day 4 and day 8. I think she'd rather stay put for longer than spending just 1 full day in each of two towns during a 4 day period.
2. Another possibility is leaving Cuzco right when we get there to go down into the sacred valley and spending a couple of nights there (perhaps at the SPG hotel in Urambamba) before heading back to Cuzco for a couple more nights. I'll probably do this one if I end up taking that Day 8 flight to cuzco.
3. Leaving Arequipa as soon as I get there to go to Chivay, and spending days 5 and 6 in the Colca Canyon before returning on Day 7. The problem with this one is it cuts out pretty much any time to actually see Arequipa. And it adds more bus time on top of already spending the entire previous night on a bus.

Does anyone have any other ideas? Should I try to do something else instead of spending 3 days in Arequipa or should I just find a way to enjoy Arequipa for 3 days?

You can do a good overview of Arequipa city just on day 5. It's enough to visit Santa Catalina monastery in the morning, and a city tour in the afternoon. Then:

Day 6. Arequipa (early bus to Colca valley, watching the beautiful landscapes, arriving 1pm aprox to Chivay town)
Day 7. Colca Canyon, condors watching, starting very early in the morning, visiting towns in the Colca Valley. around 2pm return to Arequipa city, arriving 8pm, 9pm aprox.

That fits on the new itinerary and you can fly to Cusco on day 8. and actually is the usual tour they offer. I did the 2 nights in Chivay, but actually staying 2 days/1 night is enough, The third day we spent on doing some trekking around the hills near Chivay, but it's not big deal. The 2 days visit to Colca/Chivay is maybe a bit rush but it's ok.

And in the evening day 6 in Chivay, go to the thermal hot springs pools of various temps and sip on some wine, whilst looking at a skyful of stars hanging in the crisp clean air above the mountain peaks.

Though the train is cool, I always suggest the touristic bus instead. Because it also takes the whole day (10 hours actually), but since it's faster, it stops on several places, giving the opportunity to visit Racchi ruins, the beautiful Andahuaylillas church with its painted ceiling, Puka Pukará, etc.

The train does only one stop at the highest point (included in the bus tour too).

There is a night bus Arequipa-Cuzco with Cruz del Sur, which should operate daily. Depends maybe on season. Alternatively there is a touristic bus from Colca Canyon (Chivay) to Puno similar to the one Puno-Cuzco with some touristic stops en-route.

Thanks everyone. Started doing research on the 2 day 1 night tours. It wasn't what I originally was thinking I'd want to do but it works, so crisis averted.

And since I'm arriving in Cuzco so early, I think I'll spend some time in the sacred valley right away, which is something I originally wanted to do but had to cut out.

So I lose a night of hanging out in the canyon but gain a night of hanging out in the valley.

We arrived AQP on a Friday, 11am, and did private xfer to Colca Lodge; then, on Sunday, we did the Condors. The tour company picked us up at the hotel, and took us to Yanque, where we joined a day-trip from Arequipa -- they left their hotel at 2am, rode thru the night, had breakfast in Yanque, and did the day trip of Condors, followed by the (public) thermal baths, then lunch & return.

Brutal day, but an option if you only have 1 - and can sleep on the van.

If you are really pressed, there are one day trips to Colca canyon (just to Cruz del Condor). Arequipa is worth it spending a whole day there, but 3 days are too much, especially if you don't have time

Cusco is a "hot and high" airport so flights arrive and depart early in the morning for reliability and better density altitude. (There's really good reason for all of this: my friend and cousin was on an aircraft whose crew did not respect density altitude limitations and attempted to fly out with an overloaded aircraft for current conditions, so when it lost an engine on departure from Cusco it crashed in the nearby mountains just above San Jerónimo with 8 crew and 92 passengers; only a third officer survived).

Some day in the future, there will be a larger airport in the Sacred Valley - and of course, land speculation is already rife. Maybe good to increase the number of visitors, but I am not sure this will be a good thing in the long run.

A great idea - arrive in the morning in Cusco and immediately head to the Sacred Valley. You will more likely miss soroche (acute mountain sickness) and have a chance to feel less fatigued / acclimate more easily.

Don't forget the airplane was a Lockheed L-188A Electra, not a jet, but yes they didn't respect density altitude, plus Lansa was fined also because of lack of maintenance and overloading. After few more incidents, Lansa stopped operations in 1972.

Now jets can depart from Cusco even after 4pm, but I always suggest morning flights. Not because of safety but less chance of delays. Since 2009, Cusco airport works with a PBN system, that, as I read, permits Boeings and Airbus to arrive and depart on difficult weather conditions. Right now that system is implemented in 11 peruvian airports. According to Lan Peru Mantainment and Operations manager, that helped a lot to reduce flight cancellations within Peru.

I read is near Chinchero, not within the valley but close to it. There are wide flat lands near that town, better than the current airport where the surrounding hills create strong aafternoon winds. Unfortunately the construction has not started yet so I wouldn't dare to announce an opening date.

I'm at the valley right now (San Agustin Urubamba hotel). I stayed last night at Cusco but asked the taxi drivers in the airport about transport to the s. valley. They do speak english (maybe not everybody but several do), and though are not within the airport they have their badge and are authorized drivers.

the suggested price to Urubamba is around 100 soles, to Pisaq is around 150.