My take on the equipment...Keep in mind I'm not a Hayward guy but it still applies.
Pool builder uses Hayward exclusively. I don't have enough experience to have a preference. Reviews are pro and con for both Hayward and Pentair.
Filter - Hayward makes a 525 sq ft model (C5030), Get the largest filter possible. It means less cleaning and better efficiency
I know size matters is a cartidge filter mantra around here. I'll look into the price difference. I'm already at least $5K over my expectation when designing this.
Light - There is no reason to install an incandescent light anymore. Go with at least 2 color LED lights in the pool and 1 or 2 ColorLogic lights in the reef area. You cant have enough light
Agree on the color changing LED lights, have to make the budget work with them. I'm surprised how much they cost over conventional.
Timer - Look into an automation system, especially with a spa, color changing lights and multiple pumps...Well worth the investment
I'm not certain what he's referring to with automatic pool timer, something really basic like the built-in pump control menu or something more like Pro Logic
In Floor Cleaning - Not worth the expense in my opinion. Use the savings for a robotic cleaner and automation
I know in-floor isn't a favorite here but I won't be living there for two - three years and I cant have a rover all notted up and doing circles between visits by the maintenance person.
No need for the dedicated spa pump, your 3HP main pump is sufficient to run the spa but not with 9 jets. You can get away with 6-7 jets with 3" plumbing to/from the spa. However, I would still HIGHLY recommend a second pump for your water features. I prefer variable speed pumps for this application because they allow you to fine tune the flow to your needs. If you want more than 7 spa jets, consider an additional booster pump (bring your total to 3).
I have no experience / expertise in this area so I'll defer to your knowledge in this area.
No need for a blower with a properly plumbed hartford loop in the spa
Spa light - color LED as well