OK, I'm not the most experienced Disney goer, so I'll leave the fine-tuning of your itinerary to others, but we stayed at POR at our last visit, so thought I'd chime in! We also arrived in the afternoon and didn't go to the parks that day. We checked in, explored the pool/play area, and then took the boat to Downtown Disney-- I made ADRs for Raglan Road that night. We had a blast-- I don't think that we waited long at all for the boat, and the ride itself didn't seem excessively long and was in fact a lot of fun. My dad loved Raglan Road-- he kept raving about the food, b/c he'd been to Disney the previous year with my sis and had less-than-stellar memories of Disney food. DD was enthralled by the Irish step dancers.
We used the buses every day to get to the parks and had a good experience. Usually we didn't wait long for a bus on either end. IIRC during busy times they will send different buses to POR and POFQ, so I don't remember a lot of stops in between. The one exception was coming home from AK one day, our bus also stopped at a water park. I had gotten a massive headache during the day so that particular ride was excruciating.
We went during a crowded time (our only option as we went during DH's spring break) so there wasn't much we could do with avoiding crowds & we just accepted that. I think getting there at rope drop helps- definitely seemed less crowded early morning. Also, having an ADR at Crystal Palace before rope drop was the best-- walking down a nearly-empty main street was amazing. I couldn't tell you if the crowd calendars worked (I wouldn't know the difference between an "8" and a "9") but the lines app for rides seemed pretty accurate.
Have fun-- and enjoy POR! Yes, it's spread out, but I thought the design was just beautiful. Loved all the greenery and porches on the buildings. Plus we liked being able to take an 'excursion' to POFQ and sample some beignets!
Jen, mom to "Little Miss Tiny" 4/07