no criticism intended as i hope you understand. Your ability to map out your system gives you a serious leg up on what your final design will entail and with the help of many who have made mistakes before you, your system will be much more efficient and easier to maintain.
1. Not needed. Refugium flow through typically is on the low side to allow pods and such to flourish before getting flushed into the system. This is one of my favorite areas of my system and I like the volume you have afforded it. Keep in mind that most large tank owners have been moving away from fuges with the knowledge that unless they are extremely large and well maintained, they do not provide much nutrient export. With that said, IMO, every little bit counts, and I enjoy mine as a protective enclave more so than nutrient export. It's a great place to breed live bearers and provide food for your main display, as well as to put animals that might not be socially accepted in the main tank.
2. Nevermind the perceived head pressure of raising the manifold...think about it as saving your system from flooding out during a power outage. Having the manifold above the water line, with at least one open ended feed as suggested in my other comments, will ensure that water will not back siphon and flood your tank room, removing all the water from any number of your tanks.
3. Go with the Hammerhead. You get lots more flow with room for degradation, can feed more equipment which you will inevitably add, and you should have a return line T'd immediately following the output to help with priming and evening out water levels in these various tanks. You are always welcome to PM regardig any of these issues, as I am sure many others following your build would also agree to.
4. The Vortech will provide variable flow to the frag tank that will be invaluable in controlling and acclimating various animals with different flow/light requirements.
5. enough said. Except what is the ground temp. where you are? There are many methods other than chillers to be used that are more electrically efficient. One important design to consider is a ground loop such as
Reef Haven's. One of my extra valves off my manifold is reserved for this such cooling method should I decide I need it. Give this some thought before jumping on the chiller bandwagon. With considerably fewer parts to malfunction, I believe this is a safer way to go, and I can point you towards very good pricing on the heat exchanger.
6. pull out floss shelfs are golden. I use
Aquatic-Eco Washable filter material and AFAIAC, it' sthe best you can get. It IS truly reusable and many rungs above what is generally sold in the hobby.
7. While I am a huge fan of how skillfully you drew up your plans, the first thing I would remove other than the aforementioned baffles, is virtually all the elbows. You have a sweet tank room and zero need for all that hard plumbing. Use flexible PVC and lighten the load on all of your equipment. It's much easier to install, and WAY easier to remove for cleaning. For instance, the four 1" return lines coming off my manifold are all flex PVC eliminating a large number of friction causing angles. Each one terminates with a union and a BV at the tank, so the valve can be shut and the tubing removed for cleaning. Each one can be done independently without shutting down the return pump. The manifold end of each line also terminates with a union and either a BV or a gate valve.
Here is an early stage pic of my return manifold:
Since this pic, more equipment has been installed, but I still have two extra valves for further expansion, including a ground loop if needed. The verticle line on the right is the output from my Hammerhead. Sure I lose a liitle to head pressure, but I gain significantly using the flex PVC, whle ensuring that my tank does not drain from the return lines during a power outage. If I were to buy a tank new, I would have no holes in it whatsoever, but this was a used tank and I decided to utilize four of the existing holes.
You will notice a clear PVC one-way valve. These are considered throughout the hobby as dangerous and prone to failure, but I put one in anyway primarily as a site glass to see if my return pump is operating normally. The Hammerhead is so quiet, I cannot hear if it is on. The line in the very top-right corner goes to my fuge and is above the water line. This provides a syphon break to the manifold. When the power goes out, the only water I lose is what is in the overflow and it goes into the sump.
Also keep in mind that I run my entire system off the one Hammerhead, which brings me to my third item to remove. Do you really need two main pumps? I run Vortechs for display flow and one Hammerhead for all equipment and return. I do keep a spare, but when was the last time you heard of an entire 1200+g system running on one main pump?
Give this some thought. Simpler is better. Flexible is better. Less noise, easier to work with, much less gluing, and you can always keep a coil at the ready.