A lot of people will tell you - and I agree - that when it comes to mid-day breaks it may be better to consider MK and Epcot different from AK and DHS. MK and Epcot have longer park hours so you get more bang for the buck on mid-day breaks than with AK and DHS which close earlier.
I mean, if you take a mid-day break from AK to PoR and if you leave at 1PM it could easily take an hour to get back to your room (more on that below). You get to your room by 2PM, and settle down for a nap shortly thereafter hopefully. Awake and ready to go by maybe 5PM. Then back to AK and arrive by 6PM. And the park closes by 7 or 8PM. And you still need to eat dinner. Not really worth it.
What that means for you is consider not taking taking mid-day breaks on AK and DHS days and just powering out until your kids are done for the day. And saving that wasted time going back and forth on buses.
Also, if you have not done so, it is a good idea to plan entire days to rest. Take the whole day off and stay by the pool or go to a movie at Disney Springs and stay cool in the June heat. Rebuild energy.
If you can't work in a whole day off, consider planning half days off. Maybe a late start day or two where you do not get to the parks until noon. In that case, appropriate FP+ is critical and, by the way, one of the significant benefits that FP+ offers.
Since you asked about when to make FP+ reservation, in general I advise for you to make your FP+ reservations for earlier in the day when you know you will be there. Get them all completed with the last FP+ for 1-2PM if possible (you can go right at 1PM for the last FP+ and leave the park, if you have a break planned.
With regard to PoR travel time and the 90 minute report, I have never stayed at PoR but I do know a few things:
- people tend to think of travel time as from arrival at the bus/boat/monorail (e.g., transport) stop until transport dropoff. A more fair accounting is (if you are leaving the park) the time it takes from being inside the park to get to the transport pickup location, of course waiting for the transport, then getting to your hotel and then all the way to your hotel room.
- PoR has lots of bus stops and is more spread out (which both add time), and with younger ones it can take a lot longer to walk places. Some people with teens or or only adults in their group forget or just don't know how long it can take to move around with young children.
- It is not hard for me to imagine it taking possibly 90 minutes to leave from a big park like Epcot (again with young children - so think of that taking 20-25 minutes just to get to say a bus stop from World Showcase a mile away) and get back to the hotel room at a spread out resort like PoR.
When I have long transport times like that, or want to get places where you cannot take a bus direct (say from one hotel to another) I get a taxi (or maybe Uber - never used Uber at WDW so have no idea how well it works). For $20 you can save a lot of time and that extra sleep for a child.
Finally, it is worth mentioning that for anyone who might be open to bi-coastal Disney experiences,
Disneyland Resort works much better in general for those with younger children IMO - because of the availability of nearby walking distance hotels, smaller parks and (usually) longer park hours. WDW works better as kids get older and have more energy and maybe a little more independence and do not fade every afternoon from exhaustion.