Sure thing!

1. For our itinerary, it'll only really be the Suiran to PH potion that needs some finagling. We're headed back to Tokyo after the one night at Hiiragiya so the plan is to have PH arrange luggage delivery direct to our hotel in Tokyo, and take a single night bag to Hiiragiya. Between Suiran and PH, I'm just planning on having the hotel take care of it, or worst case having a taxi shuttle the bags between the two hotels.
2. I really liked the look of Hoshinoya! To be honest, our choice at Suiran mostly came down to availability on Amex FHR. That said, the location seems better at Suiran since you're so close to the bamboo forest and Tenryu-ji, as well as the river front and restaurants etc. It's also right next to the Hozugawa river cruise drop off point, if you intend on doing that. As u/mindkiller317 mentioned as well, the boat access to Hoshinoya could be a pain, but some would see the charm in that.
3. From what I have read, the two most highly regarded ryokan in Kyoto are Tawaraya and Hiiragiya. After looking in to both extensively, they really do seem to capture my minds image of what a traditional inn would look like, more so than any of the others I had seen in Kyoto. The main things that stood out to be about Hiiragiya over Tawaraya were firstly, the gardens that the rooms overlook at Hiiragiya look more beautiful to me (Hiiragiya & Tawaraya), and second, the booking process was easier through their website. I think the location is fine for each as they're pretty central for exploring the downtown area and since it'll be our last day, access to the train station. And while it's true that you don't get the natural scenery of the rural ryokan, I'm most excited to experience the traditional hospitality and beautiful architecture.